iFull wwPDB EM Validation Report ○Aug 5, 2024 – 04:17 pm BSTPDB ID
EMDB ID
TitleAuthors
Deposited onResolution::::::9FAA
EMD-50270
Cryo-EM structure of cardiac collagen-associated amyloid AL59
Schulte, T.; Speranzini, V.; Chaves-Sanjuan, A.; Milazzo, M.; Ricagno, S.
2024-05-10
3.60 Å(reported)

This is a Full wwPDB EM Validation Report for a publicly released PDB entry.
We welcome your comments at validation@mail.wwpdb.org
A user guide is available athttps://www.wwpdb.org/validation/2017/EMValidationReportHelp
i symbol.
with specific help available everywhere you see the ○The types of validation reports are described at
http://www.wwpdb.org/validation/2017/FAQs#types.

i were used in the production of this report:
The following versions of software and data (see references ○)EMDB validation analysis
MolProbity
Percentile statistics
MapQ
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)

::
:
:
:
:
:

0.0.1.dev92
FAILED20191225.v01 (using entries in the PDB archive December 25th 2019)
1.9.13
Engh & Huber (2001)
Parkinson et al. (1996)
2.37.1

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Full wwPDB EM Validation Report

iOverall quality at a glance ○The following experimental techniques were used to determine the structure:
ELECTRON MICROSCOPY
The reported resolution of this entry is 3.60 Å.
There are no overall percentile quality scores available for this entry.
ENTRY-COMPOSITION INFOmissingINFOSEQUENCE-PLOTS INFOmissingINFO

EMD-50270, 9FAA

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EMD-50270, 9FAA

iExperimental information ○Property
EM reconstruction method
Imposed symmetry
Number of segments used
Resolution determination method
CTF correction method
Microscope
Voltage (kV)
2Electron dose (e− /Å )Minimum defocus (nm)Maximum defocus (nm)Magnification
Image detector
Maximum map value
Minimum map value
Average map value
Map value standard deviation
Recommended contour level
Map size (Å)
Map dimensions
Map angles (◦ )Pixel spacing (Å)

Value
HELICALHELICAL, twist=-0.7425◦ , rise=4.9158 Å,axial sym=C137904
FSC 0.143 CUT-OFF
PHASE FLIPPING AND AMPLITUDECORRECTIONFEI TALOS ARCTICA
20040500
2000120000
FEI FALCON III (4k x 4k)
0.090-0.050
0.000
0.003
0.02
302.26, 302.26, 302.26
340, 340, 340
90.0, 90.0, 90.0
0.88900006, 0.88900006, 0.88900006

SourceDepositor
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wwPDB
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Depositor

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EMD-50270, 9FAAi
Model quality ○iStandard geometry ○MolProbity failed to run properly - this section is therefore empty.

3.2

i
Too-close contacts ○MolProbity failed to run properly - this section is therefore empty.

3.3i
Torsion angles ○

3.3.1

i
Protein backbone ○MolProbity failed to run properly - this section is therefore empty.
3.3.2

iProtein sidechains ○MolProbity failed to run properly - this section is therefore empty.
3.3.3

i
RNA ○

MolProbity failed to run properly - this section is therefore empty.

3.4i
Non-standard residues in protein, DNA, RNA chains ○validation-pack failed to run properly - this section is therefore empty.

3.5i
Carbohydrates ○validation-pack failed to run properly - this section is therefore empty.

3.6i
Ligand geometry ○validation-pack failed to run properly - this section is therefore empty.

3.7i
Other polymers ○validation-pack failed to run properly - this section is therefore empty.

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3.8

Full wwPDB EM Validation ReportiPolymer linkage issues ○There are no chain breaks in this entry.

EMD-50270, 9FAA

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EMD-50270, 9FAAi
Map visualisation ○This section contains visualisations of the EMDB entry EMD-50270. These allow visual inspectionof the internal detail of the map and identification of artifacts.
Images derived from a raw map, generated by summing the deposited half-maps, are presented
below the corresponding image components of the primary map to allow further visual inspection
and comparison with those of the primary map.

4.1

iOrthogonal projections ○4.1.1

Primary map

X4.1.2YZYZ

Raw mapX

The images above show the map projected in three orthogonal directions.

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4.2

iCentral slices ○4.2.1

Primary map

X Index: 170

4.2.2

EMD-50270, 9FAA

Y Index: 170

Z Index: 170

Y Index: 170

Z Index: 170

Raw map

X Index: 170

The images above show central slices of the map in three orthogonal directions.

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4.3

iLargest variance slices ○4.3.1

Primary map

X Index: 185

4.3.2

EMD-50270, 9FAA

Y Index: 192

Z Index: 182

Y Index: 185

Z Index: 149

Raw map

X Index: 175

The images above show the largest variance slices of the map in three orthogonal directions.

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EMD-50270, 9FAA

4.4i
Orthogonal standard-deviation projections (False-color) ○4.4.1

Primary map

X

4.4.2

YZYZ

Raw mapX

The images above show the map standard deviation projections with false color in three orthogonal
directions. Minimum values are shown in green, max in blue, and dark to light orange shades
represent small to large values respectively.

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4.5i
Orthogonal surface views ○4.5.1

Primary map

XY

EMD-50270, 9FAA

ZThe images above show the 3D surface view of the map at the recommended contour level 0.02.
These images, in conjunction with the slice images, may facilitate assessment of whether an appropriate contour level has been provided.
4.5.2

Raw map

XYZ

These images show the 3D surface of the raw map. The raw map’s contour level was selected sothat its surface encloses the same volume as the primary map does at its recommended contour
level.

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EMD-50270, 9FAAi
Mask visualisation ○This section shows the 3D surface view of the primary map at 50% transparency overlaid with thespecified mask at 0% transparency
A mask typically either:• Encompasses the whole structure• Separates out a domain, a functional unit, a monomer or an area of interest from a largerstructure
4.6.1

i
emd_50270_msk_1.map ○XYZPage 125

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EMD-50270, 9FAAi
Map analysis ○This section contains the results of statistical analysis of the map.

5.1

i
Map-value distribution ○The map-value distribution is plotted in 128 intervals along the x-axis. The y-axis is logarithmic.
A spike in this graph at zero usually indicates that the volume has been masked.

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5.2

Full wwPDB EM Validation Report

EMD-50270, 9FAAi
Volume estimate ○The volume at the recommended contour level is 120 nm3 ; this corresponds to an approximate
mass of 108 kDa.
The volume estimate graph shows how the enclosed volume varies with the contour level. The
recommended contour level is shown as a vertical line and the intersection between the line andthe curve gives the volume of the enclosed surface at the given level.

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5.3

Full wwPDB EM Validation ReportiRotationally averaged power spectrum ○*Reported resolution corresponds to spatial frequency of 0.278 Å−1

EMD-50270, 9FAA

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EMD-50270, 9FAAi
Fourier-Shell correlation ○Fourier-Shell Correlation (FSC) is the most commonly used method to estimate the resolution ofsingle-particle and subtomogram-averaged maps. The shape of the curve depends on the imposed
symmetry, mask and whether or not the two 3D reconstructions used were processed from acommon reference. The reported resolution is shown as a black line. A curve is displayed for thehalf-bit criterion in addition to lines showing the 0.143 gold standard cut-off and 0.5 cut-off.

6.1

i
FSC ○

*Reported resolution corresponds to spatial frequency of 0.278 Å−1Page 16

6.2

Full wwPDB EM Validation ReportEMD-50270, 9FAAi
Resolution estimates ○Resolution estimate (Å)
Reported by author
Author-provided FSC curve
Unmasked-calculated*Estimation criterion (FSC cut-off )0.143 0.5
Half-bit
3.60
3.64 4.84
3.92
4.37 7.26
4.43*Resolution estimate based on FSC curve calculated by comparison of deposited half-maps. The
value from deposited half-maps intersecting FSC 0.143 CUT-OFF 4.37 differs from the reported
value 3.6 by more than 10 %Page 17

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EMD-50270, 9FAAi
Map-model fit ○This section contains information regarding the fit between EMDB map EMD-50270 and PDB
model 9FAA. Per-residue inclusion information can be found in section ?? on page ??.

7.1

i
Map-model overlay ○XYZThe images above show the 3D surface view of the map at the recommended contour level 0.02 at
50% transparency in yellow overlaid with a ribbon representation of the model coloured in blue.
These images allow for the visual assessment of the quality of fit between the atomic model andthe map.

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7.2

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EMD-50270, 9FAAi
Q-score mapped to coordinate model ○XYZThe images above show the model with each residue coloured according its Q-score. This showstheir resolvability in the map with higher Q-score values reflecting better resolvability. Please
note: Q-score is calculating the resolvability of atoms, and thus high values are only expected atresolutions at which atoms can be resolved. Low Q-score values may therefore be expected formany entries.

7.3

iAtom inclusion mapped to coordinate model ○XYZThe images above show the model with each residue coloured according to its atom inclusion. Thisshows to what extent they are inside the map at the recommended contour level (0.02).

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7.4

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EMD-50270, 9FAAi
Atom inclusion ○At the recommended contour level, 74% of all backbone atoms, 74% of all non-hydrogen atoms,
are inside the map.

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7.5

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EMD-50270, 9FAAi
Map-model fit summary ○The table lists the average atom inclusion at the recommended contour level (0.02) and Q-score
for the entire model and for each chain.
ChainAllABCDE

Atom inclusion
0.73500.74100.73600.74500.72200.7510Q-score0.45700.45700.45300.46300.44700.4630