Structure determination of small molecule compounds by an electron diffractometer for 3D ED/MicroED
Ito, Sho; White, Fraser J.; Okunishi, Eiji; Aoyama, Yoshitaka; Yamano, Akihito; Sato, Hiroyasu; Ferrara, Joseph D.; Jasnowski, Michał; Meyer, Mathias; CrystEngComm 23 (2021) 8622–8630; doi:10.1039/D1CE01172C

data_7243942
_publ_section_title
;
 Structure determination of small molecule compounds by an electron
 diffractometer for 3D ED/MicroED
;
_journal_issue                   48
_journal_name_full               CrystEngComm
_journal_page_first              8622
_journal_page_last               8630
_journal_paper_doi               10.1039/D1CE01172C
_journal_volume                  23
_journal_year                    2021
_chemical_formula_moiety         'C9 H12 N3 O5'
_chemical_formula_sum            'C9 H12 N3 O5'
_chemical_formula_weight         242.22
_chemical_name_systematic
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2021-07-13
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6272)
;
_audit_update_record
;
2021-08-31 deposited with the CCDC.	2021-10-26 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   5.1022(18)
_cell_length_b                   13.858(5)
_cell_length_c                   14.596(5)
_cell_measurement_reflns_used    638
_cell_measurement_temperature    293
_cell_measurement_theta_max      0.7567
_cell_measurement_theta_min      0.1038
_cell_volume                     1032.0(6)
_computing_cell_refinement       'CrysAlisPro 1.171.42.13a (Rigaku OD, 2021)'
_computing_data_collection       'CrysAlisPro 1.171.42.13a (Rigaku OD, 2021)'
_computing_data_reduction        'CrysAlisPro 1.171.42.13a (Rigaku OD, 2021)'
_computing_molecular_graphics    'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      293.0
_diffrn_detector                 'Rigaku HyPix-ED area detector'
_diffrn_detector_area_resol_mean 10.0
_diffrn_detector_type            'HPC area detector'
_diffrn_measured_fraction_theta_full 0.869
_diffrn_measured_fraction_theta_max 0.869
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
  1  \w    -44.00  45.00   1.00    2.00    --    0.00   0.00   0.00   89
;
_diffrn_measurement_device       'Electron diffractometer'
_diffrn_measurement_device_type  Synergy-ED
_diffrn_measurement_method       'continuous rotation'
_diffrn_radiation_probe          electron
_diffrn_radiation_type           '200 keV electrons'
_diffrn_radiation_wavelength     0.0251
_diffrn_reflns_av_R_equivalents  0.1443
_diffrn_reflns_av_unetI/netI     0.2213
_diffrn_reflns_Laue_measured_fraction_full 0.869
_diffrn_reflns_Laue_measured_fraction_max 0.869
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -4
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            2358
_diffrn_reflns_point_group_measured_fraction_full 0.874
_diffrn_reflns_point_group_measured_fraction_max 0.874
_diffrn_reflns_theta_full        0.757
_diffrn_reflns_theta_max         0.757
_diffrn_reflns_theta_min         0.104
_diffrn_source                   'thermionic-emission electron gun'
_diffrn_source_type              LaB6
_exptl_absorpt_coefficient_mu    0.000
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.55615
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.13a (Rigaku Oxford Diffraction, 2021)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.559
_exptl_crystal_description       block
_exptl_crystal_F_000             182
_exptl_crystal_size_max          0.0003
_exptl_crystal_size_mid          0.0003
_exptl_crystal_size_min          0.0003
_refine_diff_density_max         0.103
_refine_diff_density_min         -0.106
_refine_diff_density_rms         0.025
_refine_ls_abs_structure_details
;
 All f" are zero, so absolute structure could not be determined
;
_refine_ls_extinction_coef       2118(51)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.044
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     158
_refine_ls_number_reflns         1110
_refine_ls_number_restraints     132
_refine_ls_restrained_S_all      0.990
_refine_ls_R_factor_all          0.1583
_refine_ls_R_factor_gt           0.0988
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1016P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2293
_refine_ls_wR_factor_ref         0.2634
_reflns_Friedel_coverage         0.640
_reflns_Friedel_fraction_full    0.882
_reflns_Friedel_fraction_max     0.882
_reflns_number_gt                645
_reflns_number_total             1110
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1ce01172c1.cif
_cod_data_source_block           cyt2_22
_cod_depositor_comments
'Adding full bibliography for 7243939--7243951.cif.'
_cod_database_code               7243942
_shelx_shelxl_version_number     2018/3
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H,H) groups
 At 1.5 times of:
  All O(H) groups
2. Uiso/Uaniso restraints and constraints
N12 \\sim C3 \\sim C2 \\sim C1 \\sim N11 \\sim C4: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
C7 \\sim C6 \\sim O14 \\sim C5 \\sim C8: within 2A with sigma of 0.04 and sigma
for terminal atoms of 0.08 within 2A
3. Rigid body (RIGU) restrains
 N12, C3, C2, C1, N11, C4
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C7, C6, O14, C5, C8
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
4.a Ternary CH refined with riding coordinates:
 C7(H7), C6(H6), C5(H5), C8(H8)
4.b Aromatic/amide H refined with riding coordinates:
 C2(H2), C9(H9), C3(H3)
4.c X=CH2 refined with riding coordinates:
 N10(H10A,H10B)
4.d Idealised tetrahedral OH refined as rotating group:
 O15(H15), O17(H17), O16(H16)
;
_shelx_res_checksum              46239
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;