INTERNATIONAL TASK FORCE ON DEPOSITION, ARCHIVING,

**AND CURATION OF THE PRIMARY INFORMATION**

**Airlie House Meeting**

**April 4-6 2001**

**Introduction**

The structural genomics initiative will require the collection and
curation of large amounts of experimental and structural data. Each
project will collect information about all the experiments that lead to
successful (and unsuccessful) structure determinations. Once a structure
is determined, the results will be deposited into the Protein Data Bank.

**Primary Objective**

It is critical that the information that is collected by these projects
is available and usable by humans and computers, and can be archived in
the PDB in a high throughput mode. This implies that items of data
common to all projects are named consistently and represented in a
format that can be stored electronically without loss of information.
The task of this committee then becomes one of considering what data the
PDB needs to collect, and how to optimize data exchange among the
various projects and the PDB.

The primary objective requires the endorsement and cooperation of all
structural genomics projects. It will further require that each project
implements its own well thought out LIMS (Laboratory Information
Management System), and takes advantage of the experience gained by the
major genome sequencing centers in managing ambitious high throughput
projects.

**Summary of Committee Activities**

The committee considered four questions:

1\. What additional data will be collected and archived for the
structural genomics projects? These may include all aspects of the
experiments including cloning, purification, crystallization, data
collection, structure determination, structure refinement, analysis, and
function.

2\. In addition to what is already included in the current PDB, what
additional information should be included in the PDB archive? For
example, should there be more detail about data collection and structure
determination?

3\. Should there be some sort of tag that indicates that a structure has
been determined as part of a structural genomics project?

4\. Which software should be extended such that the output can be
automatically archived?

There is no final consensus yet about the answers to questions 1 and 3.
Item 4 is still being considered. A consensus was view developed
concerning 2, namely that the PDB should collect more information about
the experiment than it currently does. At present the Protein Data Bank
collects the following information:

-   Atomic coordinates

-   Structure factors

-   Journal citations

-   Names of macromolecule and ligands

```{=html}
<!-- -->
```
-   Sequence of macromolecule

-   Crystallization information

-   Unit cell and space group

-   Source information

-   Data collection information

-   Refinement information

At the meeting in Yokohama, it was suggested that the PDB collect all
information that appears in the materials and methods section of a
journal, such as the *Journal of Molecular Biology*. This committee
rigorously endorses this suggestion.

To accomplish this objective, it was first necessary to define all the
terms for the data that appear in those methods sections. The PDB staff
reviewed several articles, extracted the data items and made the
correspondences with the data dictionary that underlies the PDB. Most
aspects of the pipeline from crystallization to refinement were found in
the dictionary. The data items were sent out for review to the Task
Force ([Appendix 1]{.underline}). Several suggestions were made for
additions and modifications. These will be implemented by September 2001
after full review by the Task Force with input from other members of the
community.

The set of data items that describes protein production is not found in
the current data dictionary. A provisional list was developed and sent
to the Task Force for review. In addition, a Web site was established
for review of these items and for the submission of possible new items
(http://www-pdb.rutgers.edu:5005/). These data items involving protein
production include information about the following ([Appendix
2]{.underline}):

-   General source information

-   Production of the target gene

-   Cloning

-   Expression

-   Purification

    **Proposed Procedures and Activities**

There will be a worldwide effort to collect vast amounts of information
about proteins and their structures. In order to prevent the loss of
important information and to ensure the maximum potential collaboration
among projects, it is essential at the early stage of this effort to be
certain that information can be exchanged within and between projects.
The only way that this can happen is to come to an agreement as to which
data items are mandatory and to define each of these items carefully. A
definitive list of all data items must be finally established. This will
require thorough review by members of the Task Force as well as by other
members of the community. Once the items are agreed upon, it will be
necessary to specify clear definitions for inclusion in a data
dictionary. The plan for accomplishing this is given here.

-   Most of the data items representing the experiment from
    crystallization to structure refinement ([Appendix 1]{.underline})
    are found in the dictionary that underlies the PDB. The task force
    will attempt to reach agreement for a set of mandatory items by
    September 2001. Once that occurs these data items will become a part
    of every structural genomics projects\' submission to the PDB.

```{=html}
<!-- -->
```
-   The data items representing protein production ([Appendix
    2]{.underline}) will require more careful discussion and thought.
    Wherever possible, publicly vetted nomenclatures and controlled
    vocabularies should be used.

-   A review process has been established. Members of the structural
    genomics community will actively participate in proposing and
    reviewing these items with the goal of having a mandatory list
    established in one year's time.

```{=html}
<!-- -->
```
-   The PDB will take responsibility for the technical implementation of
    the dictionary.

```{=html}
<!-- -->
```
-   Once the mandatory data items are established, all structural
    genomics projects will deposit mandatory data to the PDB in a
    consistent format.

International Task Force on Deposition, Archiving, and Curation of the
Primary Information

# Helen M. Berman, Chair

Rutgers, The State University

Department of Chemistry

Wright and Rieman Laboratories

610 Taylor Road

Piscataway, NJ 08854-8087

Phone: 732/445-4667

Fax: 732/445-4320

e-mail: <berman@rcsb.rutgers.edu>

**Geoff Barton, Co-Chair**

EMBL-European Bioinformatics Institute

Genome Campus

Hinxton, Cambs CB10 1SD

United Kingdom

Phone: 44-1223-494414

Fax: 44-1223-494496

e-mail: <geoff@ebi.ac.uk>

# 

**Stephen Burley**

Laboratories of Molecular Biophysics &

Howard Hughes Medical Institute

The Rockefeller University

1230 York Avenue

New York, NY 10021

Phone: 212/327-8336

Fax: 212/327-8337

e-mail: burley@rockvax.rockefeller.edu

**Aled Edwards**

Banting and Best Department of Medical Research

CH Best Institute Rm. 402

University of Toronto 112 College Street

Toronto, Ontario M5G 1L6 Canada

Phone: 00 1 416 946 3436

Fax: 00 1 416 978 8528

e-mail: aled.edwards@utoronto.ca

**Udo Heinemann**

Max-Delbruck Center for Molecular Medicine

Robert-Roessle-Str. 10

D-13122 Berlin, Germany

Phone: 49 30 94063420

Fax: 49 30 94062548

e-mail: heinemann@mdc-berlin.de

#  Haruki Nakamura

Biomolecular Engineering Research Institute

6-2-3 Furuedai, Suita

Osaka, 565-0874 Japan

Phone: 06 872 8212

Fax: 06 872 8219

e-mail: nakamura@beri.co.jp

**Osnat Herzberg**

Center for Advanced Research in Biotechnology

University of Maryland Biotechnology Institute

9600 Gudelsky Drive

Rockville, MD 20850

Phone: 301/738-6245

Fax: 301/738-6255

e-mail: osnat@carb.nist.gov

**Andrzej Joachimiak**

Dept of Struct Bio Center

Argonne National Lab

9700 S Cass Ave 202/Q118

Argonne, IL 60439

Phone: 630/252-6126

Fax: 630/252-3926

e-mail: <andrzejj@anl.gov>

**Sung-Hou Kim**

Professor of Biophysical Chemistry

Department of Chemistry

University of California

Berkeley, CA 94720

Phone: 510/486-4333

Fax: 510/486-5272

e-mail: shkim@lbl.gov

**Guy (Gaetano) Montelione**

Rutgers University

Dept of Molecular Biology and Biochemistry

CABM, Rm. 014A

679 Hoes Lane

Piscataway, NJ 08854

Phone: 732/235-5321

Fax: 732/235-4850

e-mail: guy@nmrlab.cabm.rutgers.edu

# Dino Moras

UPR de Biologie Structurale

IGBMC

1 rue Laurent Fries

BP 163

67404 Illkirch Cedex

France

Phone: 33 388653351

Fax: 33 388653276

e-mail: moras@igbmc.u-strasbg.fr

# John Rose

Dept of Biochemistry & Molecular Biology

University of Georgia

Athens, GA 30602

Phone: 706 542 1750

Fax: 706 542 3077

e-mail: rose@bcL4.bmb.uga.edu

# Joel L. Sussman

Kimmelman Center for Biomolecular

Structure and Assembly

Department of Structural Chemistry

The Weizmann Institute of Science

Rehovot 76100

Israel

Phone: 972 8 934 2638

Fax: 972 8 934 4159

e-mail: <joel@sgjs3.weizmann.ac.il>

**Thomas C Terwilliger**

Struct Bio Group

Los Alamos National Lab

Mail Stop M880

Los Alamos, NM 87545

Phone: 505/667-0072

Fax: 505/665-3024

e-mail: terwilliger@lanl.gov

**Eldon Ulrich**

BioMagResBank

University of Wisconsin-Madison

Department of Biochemistry

420 Henry Mall

Madison, WI 53706

Phone: 608-265-5741

Fax: 608-262-3453

e-mail: elu@bmrb.wisc.edu

**Bi-Cheng Wang**

Dept of Biochem & Molecular Biology

University of Georgia

Life Sciences Building

Athens, GA 30602-7229

Phone: 706/542-1747

Fax: 706/542-3077

e-mail: wang@bcl1.bmb.uga.edu

**Ian Wilson**

The Scripps Research Institute

Molecular Biology

10550 North Torrey Pines Road

La Jolla, CA 92037

Phone: 858/784-9706

Fax: 858/784-2980

e-mail: wilson@scripps.edu

**Shigeyuki Yokoyama**

Protein Research Group

RIKEN Genomic Sciences Centre

1-7-22 Suehiro-cho, Tsurumi, Yokohama

230-0045, JAPAN

Phone: 81 45 503 9196

Fax: 81 45 503 9195

e-mail: yokoyama@biochem.s.u-tokyo.ac.jp

**Appendix 1: DATA ITEMS REPRESENTED IN PAPERS DESCRIBING COMPLETED
STRUCTURES**

MACROMOLECULE NAME:

+-----------------------------------+-----------------------------------+
|                                   |                                   |
+-----------------------------------+-----------------------------------+
| Molecule name                     | \_entity.pdbx_description holds   |
|                                   | the name corresponding to PDB     |
|                                   | compound name.                    |
|                                   |                                   |
|                                   | Multiple systematic and common    |
|                                   | names can be supplied in mmCIF    |
|                                   | categories                        |
|                                   |                                   |
|                                   | entity_name_sys and               |
|                                   | entity_name_com                   |
+-----------------------------------+-----------------------------------+
| Fragment                          | \_entity_keywords.pdbx_fragment   |
+-----------------------------------+-----------------------------------+
| Mutations                         | \_entity_keywords.pdbx_mutation   |
+-----------------------------------+-----------------------------------+
| E.C. number                       | \_entity_keywords.pdbx_ec         |
+-----------------------------------+-----------------------------------+

Notes: Macromolecule names are recorded in PDB COMPND records. All of
the above items are included in the current format. The assignment of
multiple common and systematic names is supported by mmCIF but not in
the PDB format.

CRYSTALLIZATION CONDITIONS AND UNIT CELL PARAMETERS:

+-----------------------------------+-----------------------------------+
| Data Item                         | Dictionary Item Name              |
+-----------------------------------+-----------------------------------+
| Crystallization method            | \_exptl_crystal_grow.method       |
+-----------------------------------+-----------------------------------+
| Apparatus                         | \_exptl_crystal_grow.apparatus    |
+-----------------------------------+-----------------------------------+
| Temperature                       | \_exptl_crystal_grow.temp         |
|                                   |                                   |
|                                   | \_exptl_crystal_grow.temp_details |
+-----------------------------------+-----------------------------------+
| pH                                | \_exptl_crystal_grow.pH           |
|                                   |                                   |
|                                   | \                                 |
|                                   | _exptl_crystal_grow.pdbx_pH_range |
+-----------------------------------+-----------------------------------+
| Crystallization solution          | Tabulated in mmCIF category       |
| compositions                      |                                   |
|                                   | exptl_crystal_grow_comp           |
+-----------------------------------+-----------------------------------+
| Additional treatments (e.g.       | \_exptl_crystal.preparation       |
| soaking)                          |                                   |
+-----------------------------------+-----------------------------------+
| Cell constants                    | \_cell.length_a                   |
|                                   |                                   |
|                                   | \_cell.length_b                   |
|                                   |                                   |
|                                   | \_cell.length_c                   |
|                                   |                                   |
|                                   | \_cell.length_alpha               |
|                                   |                                   |
|                                   | \_cell.length_beta                |
|                                   |                                   |
|                                   | \_cell.length_gamma               |
+-----------------------------------+-----------------------------------+
| Space Group                       | \_symmetry.space_group_name_H-M   |
+-----------------------------------+-----------------------------------+

Notes: Crystallization conditions are recorded as free text in PDB
REMARK 280. Cell constants are recorded on the PDB CRYST1 records. mmCIF
provides for description of multiple crystals and maintains the
correspondences between each crystal and its associated diffraction data
sets.

SOURCE INFORMATION:

  ------------------------------ --------------------------------------------------
  Data Item                      Dictionary Item Name

  Organism common name           \_entity_src_gen.gene_src_common_name

  Organism scientific name       \_entity_src_gen.pdbx_gene_src_scientific_name

  Organ                          \_entity_src_gen.pdbx_gene_src_organ

  Gene                           \_entity_src_gen.pdbx_gene_src_gene

  Cellular location              \_entity_src_gen.pdbx_gene_src_cellular_location

                                 

  Expression system common name  \_entity_src_gen.host_org_common_name

  Expression system scientific   \_entity_src_gen.pdbx_host_org_scientific_name
  name                           

  Expression system cell line    \_entity_src_gen.pdbx_host_org_cell_line

  Expression system strain       \_entity_src_gen.pdbx_host_org_strain

  Expression system variant      \_entity_src_gen.pdbx_host_org_variant

  Expression vector              \_entity_src_gen.pdbx_host_org_vector

  Expression plasmid             \_entity_src_gen.plasmid_name

  Expression system cellular     \_entity_src_gen.pdbx_host_org_cellular_location
  location                       

  Expression system gene         \_entity_src_gen.pdbx_host_org_gene
  ------------------------------ --------------------------------------------------

Notes: Source information is recorded in PDB SOURCE records. All of the
above source items are represented in the current format.

DATA COLLECTION:

+----------------------------------+-----------------------------------+
|                                  |                                   |
+----------------------------------+-----------------------------------+
| Data collection site             | \_di                              |
|                                  | ffrn_source.pdbx_synchrotron_site |
+----------------------------------+-----------------------------------+
| Beamline                         | \_diffrn                          |
|                                  | _source.pdbx_synchrotron_beamline |
+----------------------------------+-----------------------------------+
| Detector                         | \_diffrn_detector.detector        |
|                                  |                                   |
|                                  | \_diffrn_detector.type            |
+----------------------------------+-----------------------------------+
| Collection temperature           | \_diffrn.ambient_temp             |
|                                  |                                   |
|                                  | \_diffrn.ambient_temp_details     |
+----------------------------------+-----------------------------------+
| Total unique reflections         | \_reflns.number_all               |
| collected                        |                                   |
+----------------------------------+-----------------------------------+
| Observed reflections (\> Sigma   | \_reflns.number_obs               |
| cutoff)                          |                                   |
+----------------------------------+-----------------------------------+
| Criterion for "observed"         | \_reflns.observed_criterion       |
| reflections                      |                                   |
+----------------------------------+-----------------------------------+
| Wavelength(s) used (simplified)  | \_diff                            |
|                                  | rn_radiation.pdbx_wavelength_list |
+----------------------------------+-----------------------------------+
| Wavelength(s) used (detailed)    | \_diffr                           |
|                                  | n_radiation_wavelength.wavelength |
+----------------------------------+-----------------------------------+
| Resolution range                 | \_reflns.d_resolution_high        |
|                                  |                                   |
|                                  | \_reflns.d_resolution_low         |
+----------------------------------+-----------------------------------+
| Completeness (observed)          | \_reflns.percent_possible_obs     |
+----------------------------------+-----------------------------------+
| Completeness of high resolution  | \_                                |
| shell                            | reflns_shell.percent_possible_obs |
+----------------------------------+-----------------------------------+
| Redundancy overall               | \_reflns.pdbx_redundancy          |
+----------------------------------+-----------------------------------+
| Redundancy for high resolution   | \_reflns_shell.pdbx_redundancy    |
| shell                            |                                   |
+----------------------------------+-----------------------------------+
| R-Merge (overall observed)       | \_reflns.Rmerge_F_obs             |
|                                  |                                   |
|                                  | \_reflns.pdbx_Rmerge_I_obs        |
+----------------------------------+-----------------------------------+
| R-Merge (high resolution shell)  | \_reflns_shell.Rmerge_F_obs       |
|                                  |                                   |
|                                  | \_reflns_shell.Rmerge_I_obs       |
+----------------------------------+-----------------------------------+
| R-Symm                           | \_reflns.pdbx_Rsym_value          |
|                                  |                                   |
|                                  | \_reflns_shell.pdbx_Rsym_value    |
+----------------------------------+-----------------------------------+
| \<I\> over \<sigma I\>           | \_reflns.pdbx_netI_over_av_sigmaI |
|                                  |                                   |
|                                  | \_reflns_shell.meanI_over_sigI    |
+----------------------------------+-----------------------------------+
| Data processing software         | mmCIF category "software"         |
|                                  | provides for                      |
|                                  |                                   |
|                                  | complete program description.     |
+----------------------------------+-----------------------------------+

Notes: Data collection details are recorded in PDB REMARK 200. The
description above provides a summary of the collected data with respect
to the solved structure. If the data are originally encoded in
imgCIF/CBF, then much greater detail is available describing the
diffraction data sets that contributes to the final merged data set.

STRUCTURE SOLUTION AND PHASING:

+----------------------------------+-----------------------------------+
|                                  |                                   |
+----------------------------------+-----------------------------------+
| For each MAD data set:           |                                   |
+----------------------------------+-----------------------------------+
| Wavelength                       | \_phasing_MAD_set.wavelength      |
+----------------------------------+-----------------------------------+
| Resolution range                 | \_phasing_MAD_set.d_res_high      |
|                                  |                                   |
|                                  | \_phasing_MAD_set.d_res_low       |
+----------------------------------+-----------------------------------+
| f'                               | \_phasing_MAD_set.f_prime         |
+----------------------------------+-----------------------------------+
| f''                              | \_phasing_MAD_set.f_double_prime  |
+----------------------------------+-----------------------------------+
| \<FOM\>                          | \_phasing_MAD_expt.mean_fom       |
+----------------------------------+-----------------------------------+
| R-Cullis (acentric)              |                                   |
+----------------------------------+-----------------------------------+
| R-Cullis (centric)               |                                   |
+----------------------------------+-----------------------------------+
| R-Cullis (anomalous)             |                                   |
+----------------------------------+-----------------------------------+
| Phasing power (acentric)         |                                   |
+----------------------------------+-----------------------------------+
| Phasing power (centric)          |                                   |
+----------------------------------+-----------------------------------+
|                                  |                                   |
+----------------------------------+-----------------------------------+
| For each MIR data set:           |                                   |
+----------------------------------+-----------------------------------+
| Resolution range                 | \_phasing_MIR_der.d_res_high      |
|                                  |                                   |
|                                  | \_phasing_MIR_der.d_res_low       |
+----------------------------------+-----------------------------------+
| Number of sites                  | \_phasing_MIR_der.number_of_sites |
+----------------------------------+-----------------------------------+
| Power acentric                   | \_phasing_MIR_der.power_acentric  |
+----------------------------------+-----------------------------------+
| Power centric                    | \_phasing_MIR_der.power_centric   |
+----------------------------------+-----------------------------------+
| R-Cullis (acentric)              | \_                                |
|                                  | phasing_MIR_der.R_cullis_acentric |
+----------------------------------+-----------------------------------+
| R-Cullis (centric)               | \                                 |
|                                  | _phasing_MIR_der.R_cullis_centric |
+----------------------------------+-----------------------------------+
| R-Cullis (anomalous)             | \_p                               |
|                                  | hasing_MIR_der.R_cullis_anomalous |
+----------------------------------+-----------------------------------+
| \<FOM\> (overall)                | \_phasing_MIR.FOM                 |
+----------------------------------+-----------------------------------+
| \<FOM\> (high resolution shell)  | \_phasing_MIR_der_shell.fom       |
+----------------------------------+-----------------------------------+
|                                  |                                   |
+----------------------------------+-----------------------------------+
| Structure solution software      | mmCIF category "software"         |
|                                  | provides for                      |
|                                  |                                   |
|                                  | complete program description.     |
+----------------------------------+-----------------------------------+

Notes: The details are MAD and MIR experiments are not captured in the
current PDB data file.

REFINEMENT INFORMATION**:**

+---------------------------------+------------------------------------+
| Data Item                       | Dictionary Item Name               |
+---------------------------------+------------------------------------+
| Resolution range                | \_refine.ls_d_res_low              |
|                                 |                                    |
|                                 | \_refine.ls_d_res_high             |
+---------------------------------+------------------------------------+
| Resolution range (highest res.  | \_refine_ls_shell.d_res_low        |
| shell)                          |                                    |
|                                 | \_refine_ls_shell.d_res_high       |
+---------------------------------+------------------------------------+
| Number of reflections used in   | \_refine.ls_number_reflns_obs      |
| refinement                      |                                    |
+---------------------------------+------------------------------------+
| Number of reflections in R-Free | \_refine.ls_number_reflns_R_free   |
| set                             |                                    |
+---------------------------------+------------------------------------+
| R-factor                        | \_refine.ls_R_factor_R_work        |
|                                 |                                    |
|                                 | \_refine.ls_R_factor_R_free        |
+---------------------------------+------------------------------------+
| Number of atoms refined         | \_refine_hist.number_atoms_total   |
|                                 |                                    |
|                                 | \_refine_hist.number_atoms_solvent |
|                                 |                                    |
|                                 | \_ref                              |
|                                 | ine_hist.pdbx_number_atoms_protein |
|                                 |                                    |
|                                 | \_refine_h                         |
|                                 | ist.pdbx_number_atoms_nucleic_acid |
|                                 |                                    |
|                                 | \_re                               |
|                                 | fine_hist.pdbx_number_atoms_ligand |
+---------------------------------+------------------------------------+
| RMS Bond Distances              | \_refine_ls_restr.type             |
|                                 | \_refine_ls_restr.dev_ideal_target |
|                                 |                                    |
|                                 | \_refine_ls_restr.dev_ideal        |
+---------------------------------+------------------------------------+
| RMS Bond Angles                 |                                    |
+---------------------------------+------------------------------------+
| RMS Chiral Volume               |                                    |
+---------------------------------+------------------------------------+
| RMS Planar Torsion Angles       |                                    |
+---------------------------------+------------------------------------+
| RMS Staggered Torsion Angles    |                                    |
+---------------------------------+------------------------------------+
| RMS Orthonormal Torsion Angles  |                                    |
+---------------------------------+------------------------------------+
|                                 |                                    |
+---------------------------------+------------------------------------+
| Isotropic temperature factor    | \_refine_b_iso.class               |
| restraints                      |                                    |
|                                 | \_refine_b_iso.treatment           |
|                                 |                                    |
|                                 | \_refine_b_iso.value               |
+---------------------------------+------------------------------------+
| Non-crystallographic symmetry   | NCS related domains are described  |
| restraints                      | in mmCIF categories struct_ncs_dom |
|                                 | and struct_ncs_dom_lim.            |
|                                 |                                    |
|                                 | The ncs operations relating the    |
|                                 | domain ensembles are described in  |
|                                 | categories struct_ncs_ens,         |
|                                 | struct_ncs_ens_gen, and            |
|                                 | struct_ncs_oper. NCS restraints    |
|                                 | used in refinement are described   |
|                                 | in                                 |
|                                 |                                    |
|                                 | category refine_ls_restr_ncs.      |
+---------------------------------+------------------------------------+
| Solvent model used              | \_refine.solvent_model_details     |
|                                 |                                    |
|                                 | \_refine.solvent_model_param_bsol  |
|                                 |                                    |
|                                 | \_refine.solvent_model_param_ksol  |
+---------------------------------+------------------------------------+
| Starting model                  | \_refine.pdbx_starting_model       |
+---------------------------------+------------------------------------+
| Overall Average Isotropic B     | \_refine.B_iso_mean                |
| Factor                          |                                    |
+---------------------------------+------------------------------------+
| Overall Anisotropic B Factor    | \_refine.aniso_B\[1\]\[1\]         |
|                                 |                                    |
|                                 | \_refine.aniso_B\[1\]\[2\]         |
|                                 |                                    |
|                                 | \_refine.aniso_B\[1\]\[3\]         |
|                                 |                                    |
|                                 | \_refine.aniso_B\[2\]\[2\]         |
|                                 |                                    |
|                                 | \_refine.aniso_B\[2\]\[3\]         |
|                                 |                                    |
|                                 | \_refine.aniso_B\[3\]\[3\]         |
+---------------------------------+------------------------------------+
| Overall Isotropic B Factor      | Computed from                      |
|                                 | \_atom_site.B_iso_or_equiv         |
| \+ main chain atoms             |                                    |
|                                 |                                    |
| \+ side chain atoms             |                                    |
|                                 |                                    |
| \+ ligand atoms                 |                                    |
|                                 |                                    |
| \+ solvent                      |                                    |
+---------------------------------+------------------------------------+
| Refinement software             | mmCIF category "software" provides |
|                                 | for                                |
|                                 |                                    |
|                                 | complete program description.      |
+---------------------------------+------------------------------------+
| Stereochemical                  |                                    |
| quality/Ramachandran analysis   |                                    |
|                                 |                                    |
| \+ number of residues in        |                                    |
| favored regions                 |                                    |
|                                 |                                    |
| \+ number of residues in        |                                    |
| additionally                    |                                    |
|                                 |                                    |
| allowed regions                 |                                    |
|                                 |                                    |
| \+ number of residues in        |                                    |
| generously allowed              |                                    |
|                                 |                                    |
| regions                         |                                    |
|                                 |                                    |
| \+ number of residues in        |                                    |
| disallowed regions              |                                    |
+---------------------------------+------------------------------------+

Notes: Refinement details are recorded in PDB REMARK 3. All of the above
refinement parameters, except the Ramachandran analysis, are included in
the current PDB format file. Matrices describing NCS operations are
recorded in PDB MTRIX records. There are many more data items associated
with refinement defined in the mmCIF dictionary that could be easily
captured

(e.g. refinement statistics for each resolution shell).

**Appendix 2: DATA ITEMS FOR PROTEIN PRODUCTION**

GENERAL SOURCE INFORMATION:

  ------------------------------- --------------------------------------------------
  **Data Item**                   **Dictionary Item Name**

  **Organism common name**        \_entity_src_gen.gene_src_common_name

  **Organism scientific name**    \_entity_src_gen.pdbx_gene_src_scientific_name

  **Organ**                       \_entity_src_gen.pdbx_gene_src_organ

  **Gene**                        \_entity_src_gen.pdbx_gene_src_gene

  **Cellular location**           \_entity_src_gen.pdbx_gene_src_cellular_location

                                  

  **Expression system common      \_entity_src_gen.host_org_common_name
  name**                          

  **Expression system scientific  \_entity_src_gen.pdbx_host_org_scientific_name
  name**                          

  **Expression system cell line** \_entity_src_gen.pdbx_host_org_cell_line

  **Expression system strain**    \_entity_src_gen.pdbx_host_org_strain

  **Expression system variant**   \_entity_src_gen.pdbx_host_org_variant

  **Expression vector**           \_entity_src_gen.pdbx_host_org_vector

  **Expression plasmid**          \_entity_src_gen.plasmid_name

  **Expression system cellular    \_entity_src_gen.pdbx_host_org_cellular_location
  location**                      

  **Expression system gene**      \_entity_src_gen.pdbx_host_org_gene
  ------------------------------- --------------------------------------------------

PRODUCTION OF THE TARGET GENE:

  ------------------------------- ---------------------------------------------------
  **Data Item**                   **Dictionary Item Name**

  **Source organism or original   \_entity_src_gen.gene_src_common_name
  gene**                          

                                  \_entity_src_gen.pdbx_gene_src_scientific_name

                                  

  **PCR step number**             \_entity_src_gen_prod_pcr.step_id

  **PCR gene source**             \_entity_src_gen_prod_pcr.gene_source

  **Forward PCR primer sequence   \_entity_src_gen_prod_pcr.forward_primer_sequence
  (5')**                          

  **Reverse PCR primer sequence   \_entity_src_gen_prod_pcr.reverse_primer_sequence
  (3')**                          

  **PCR reaction conditions**     \_entity_src_gen_prod_pcr.reaction_details

  **PCR purification details**    \_entity_src_gen_prod_pcr.purification_details

  **Overall production step       \_entity_src_gen_prod_pcr.prod_step_id
  number**                        

                                  

  **Digestion step number**       \_entity_src_gen_prod_digest.step_id

  **First digestion restriction   \_entity_src_gen_prod_digest.restriction_site_1
  site**                          

  **Second digestion restriction  \_entity_src_gen_prod_digest.restriction_site_2
  site**                          

  **Purification of gene          \_entity_src_gen_prod_digest.purification_details
  product**                       

  **Overall production step       \_entity_src_gen_prod_digest.prod_step_id
  number \[1\]**                  
  ------------------------------- ---------------------------------------------------

\[1\] Step number in the overall protein production process. This item
is provided to

allow the sequence of production operations to be recorded.

BACTERIAL CLONING:

  ----------------------------- ------------------------------------------------------
  **Data Item**                 **Dictionary Item Name**

                                

  **Cloning vector**            \_entity_src_gen.pdbx_host_org_vector

  **Plasmid name**              \_entity_src_gen.plasmid_name

  **Enzyme(s) used to prepare   \_entity_src_gen_bact_clone.cleavage_enzymes
  vector**                      

  **Vector purification         \_entity_src_gen_bact_clone.purification_details
  details**                     

  **Enzymes used for ligation** \_entity_src_gen_bact_clone.ligation_enzymes

  **Ligation temperature**      \_entity_src_gen_bact_clone.ligation_temperature

  **Ligation time**             \_entity_src_gen_bact_clone.ligation_time

  **Transformation method**     \_entity_src_gen_bact_clone.transformation_method

  **Clone selection marker**    \_entity_src_gen_bact_clone.clone_marker

  **Clone selection criteria**  \_entity_src_gen_bact_clone.clone_selection_criteria

  **Overall production step     \_entity_src_gen_bact_clone.prod_step_id
  number**                      
  ----------------------------- ------------------------------------------------------

BACTERIAL EXPRESSION:

  ----------------------------- -----------------------------------------------------
  **Data Item**                 **Dictionary Item Name**

                                

  **Promoter type**             \_entity_src_gen_bact_express.promoter_type

  **Gene insertion length**     \_entity_src_gen_bact_express.gene_insert_length

  **Gene mutations**            \_entity_src_gen_bact_express.gene_mutations

  **N-terminal sequence tags**  \_entity_src_gen_bact_express.N_terminal_seq_tag

  **C-terminal sequence tags**  \_entity_src_gen_bact_express.C_terminal_seq_tag

  **Culture base media**        \_entity_src_gen_bact_express.culture_base_media

  **Culture additives**         \_entity_src_gen_bact_express.culture_additives

  **Culture volume**            \_entity_src_gen_bact_express.culture_volume

  **Culture time**              \_entity_src_gen_bact_express.culture_time

  **Induction procedure**       \_entity_src_gen_bact_express.induction_details

  **Induction timepoint**       \_entity_src_gen_bact_express.induction_timepoint

  **Growth time after           \_entity_src_gen_bact_express.induction_growth_time
  induction**                   

  **Protein location**          \_entity_src_gen_bact_express.protein_location

  **Harvesting protocol**       \_entity_src_gen_bact_express.harvesting_details

  **Storage conditions**        \_entity_src_gen_bact_express.storage_details

  **Overall production step     \_entity_src_gen_bact_express.prod_step_id
  number**                      
  ----------------------------- -----------------------------------------------------

PURIFICATION:

  ----------------------------- -----------------------------------------------------
  **Data Item**                 **Dictionary Item Name**

  **Assay methods**             \_entity_src_gen_pure.assay_method_details

  **Purification preparation    \_entity_src_gen_pure.preparation_scale
  scale**                       

                                

  **Lysis method**              \_entity_src_gen_pure_lysis.method_details

  **Lysis buffer composition**  \_entity_src_gen_pure_lysis.buffer

  **Lysis buffer volume**       \_entity_src_gen_pure_lysis.buffer_volume

  **Lysis temperature**         \_entity_src_gen_pure_lysis.temperature

  **Lysis separation details**  \_entity_src_gen_pure_lysis.separation_details

  **Overall production step     \_entity_src_gen_pure_lysis.prod_step_id
  number**                      

                                

  **Fractionation step number** \_entity_src_gen_pure_fract.step_id

  **Fractionation method**      \_entity_src_gen_pure_fract.method_details

  **Fractionation temperature** \_entity_src_gen_pure_fract.temperature

  **Fractionation separation    \_entity_src_gen_pure_fract.separation_details
  details**                     

  **Protein location**          \_entity_src_gen_pure_fract.protein_location

  **Overall production step     \_entity_src_gen_pure_fract.prod_step_id
  number**                      

                                

  **Chromatographic step        \_entity_src_gen_pure_chrom.step_id
  number**                      

  **Column type**               \_entity_src_gen_pure_chrom.column_type

  **Column volume**             \_entity_src_gen_pure_chrom.column_volume

  **Temperature**               \_entity_src_gen_pure_chrom.column_temperature

  **Equilibration buffer**      \_entity_src_gen_pure_chrom.equilibration_buffer

  **Elution protocol**          \_entity_src_gen_pure_chrom.elution_protocol

  **Sample preparation**        \_entity_src_gen_pure_chrom.sample_prep_details

  **Sample volume**             \_entity_src_gen_pure_chrom.sample_volume

  **Sample amount**             \_entity_src_gen_pure_chrom.sample_amount

  **Volume of pooled            \_entity_src_gen_pure_chrom.volume_pooled_fractions
  fractions**                   

  **Yield of pooled fractions** \_entity_src_gen_pure_chrom.yield_pooled_fractions

  **Overall production step     \_entity_src_gen_pure_chrom.prod_step_id
  number**                      

                                

  **Concentration procedure**   \_entity_src_gen_pure.concentration_details

  **Concentration device**      \_entity_src_gen_pure.concentration_device

  **Final storage buffer**      \_entity_src_gen_pure.storage_buffer

  **Final storage temperature** \_entity_src_gen_pure.storage_temperature

  **Final protein               \_entity_src_gen_pure.protein_concentration
  concentration**               

  **Protein conc. measurement   \_entity_src_gen_pure.protein_measurement_details
  method**                      
  ----------------------------- -----------------------------------------------------