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_7243948
_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_absolute_configuration unk
_chemical_formula_moiety         'C6 H12 O6'
_chemical_formula_sum            'C6 H12 O6'
_chemical_formula_weight         180.16
_chemical_name_systematic
(3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol
_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
_atom_sites_solution_primary     dual
_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                   5.177(2)
_cell_length_b                   10.691(5)
_cell_length_c                   15.272(7)
_cell_measurement_reflns_used    496
_cell_measurement_temperature    293
_cell_measurement_theta_max      0.7989
_cell_measurement_theta_min      0.1157
_cell_volume                     845.3(6)
_computing_cell_refinement       'CrysAlisPro 1.171.42.18a (Rigaku OD, 2021)'
_computing_data_collection       'CrysAlisPro 1.171.42.18a (Rigaku OD, 2021)'
_computing_data_reduction        'CrysAlisPro 1.171.42.18a (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
_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 0.742
_diffrn_measured_fraction_theta_max 0.742
_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    -30.00  30.00   1.00    4.00    --    0.00   0.00   0.00   60
;
_diffrn_measurement_device       'Electron diffractometer'
_diffrn_measurement_device_type  Rigaku_Synergy-ED
_diffrn_measurement_method       'continuous rotation'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0003981000
_diffrn_orient_matrix_UB_12      -0.0012348000
_diffrn_orient_matrix_UB_13      0.0013903000
_diffrn_orient_matrix_UB_21      -0.0022529000
_diffrn_orient_matrix_UB_22      0.0017223000
_diffrn_orient_matrix_UB_23      0.0008238000
_diffrn_orient_matrix_UB_31      -0.0042744000
_diffrn_orient_matrix_UB_32      -0.0010107000
_diffrn_orient_matrix_UB_33      -0.0002996000
_diffrn_radiation_probe          electron
_diffrn_radiation_type           '200 keV electrons'
_diffrn_radiation_wavelength     0.0251
_diffrn_reflns_av_R_equivalents  0.0934
_diffrn_reflns_av_unetI/netI     0.1213
_diffrn_reflns_Laue_measured_fraction_full 0.742
_diffrn_reflns_Laue_measured_fraction_max 0.742
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -5
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       14
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            1519
_diffrn_reflns_point_group_measured_fraction_full 0.773
_diffrn_reflns_point_group_measured_fraction_max 0.773
_diffrn_reflns_theta_full        0.799
_diffrn_reflns_theta_max         0.799
_diffrn_reflns_theta_min         0.116
_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  0.76258
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.18a (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    1.416
_exptl_crystal_description       block
_exptl_crystal_F_000             133
_exptl_crystal_size_max          0.0001
_exptl_crystal_size_mid          0.0001
_exptl_crystal_size_min          0.0001
_refine_diff_density_max         0.120
_refine_diff_density_min         -0.145
_refine_diff_density_rms         0.042
_refine_ls_abs_structure_details
;
 All f" are zero, so absolute structure could not be determined
;
_refine_ls_extinction_coef       1968(52)
_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   1.156
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     115
_refine_ls_number_reflns         938
_refine_ls_number_restraints     159
_refine_ls_restrained_S_all      1.069
_refine_ls_R_factor_all          0.1663
_refine_ls_R_factor_gt           0.1194
_refine_ls_shift/su_max          0.005
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1413P)^2^+0.4402P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3194
_refine_ls_wR_factor_ref         0.3469
_reflns_Friedel_coverage         0.705
_reflns_Friedel_fraction_full    0.820
_reflns_Friedel_fraction_max     0.820
_reflns_number_gt                600
_reflns_number_total             938
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1ce01172c1.cif
_cod_data_source_block           d-glucose_003
_cod_depositor_comments
'Adding full bibliography for 7243939--7243951.cif.'
_cod_original_cell_volume        845.3(7)
_cod_database_code               7243948
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C6 H12 O6'
_reflns_odcompleteness_completeness 73.39
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     0.80
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All O(H) groups
2. Uiso/Uaniso restraints and constraints
O10 \\sim C5 \\sim C4 \\sim O9 \\sim C3 \\sim O8 \\sim O7 \\sim C2 \\sim C1
\\sim C6 \\sim O12 \\sim O11: within 2A with sigma of 0.04 and sigma for
terminal atoms of 0.08 within 2A
3. Rigid body (RIGU) restrains
 O9, C4, C3, O8, C2, O7, C1, O11, C5, O10, C6, O12
 with sigma for 1-2 distances of 0.003 and sigma for 1-3 distances of 0.003
4.a Ternary CH refined with riding coordinates:
 C3(H3), C4(H4), C5(H5), C2(H2), C1(H1)
4.b Secondary CH2 refined with riding coordinates:
 C6(H6A,H6B)
4.c Idealised tetrahedral OH refined as rotating group:
 O7(H7), O10(H10), O9(H9), O8(H8), O12(H12)
;
_shelx_res_checksum              6305
_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
;
_oxdiff_exptl_absorpt_empirical_full_max 1.253
_oxdiff_exptl_absorpt_empirical_full_min 0.635