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_7243943
_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         'C24 H18'
_chemical_formula_sum            'C24 H18'
_chemical_formula_weight         306.38
_chemical_name_systematic        1,3,5-triphenylbenzene
_space_group_crystal_system      orthorhombic
_space_group_IT_number           33
_space_group_name_Hall           'P 2c -2n'
_space_group_name_H-M_alt        'P n a 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                   7.8(5)
_cell_length_b                   20.2(2)
_cell_length_c                   11.5(2)
_cell_measurement_reflns_used    486
_cell_measurement_temperature    293
_cell_measurement_theta_max      0.8780
_cell_measurement_theta_min      0.1170
_cell_volume                     1812(12)
_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    'SHELXD  (Sheldrick, 2008)'
_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 0.803
_diffrn_measured_fraction_theta_max 0.803
_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    -50.00  35.00   1.00   10.00    --    0.00   0.00   0.00   85
;
_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      -0.0031402000
_diffrn_orient_matrix_UB_12      0.0000081000
_diffrn_orient_matrix_UB_13      -0.0005046000
_diffrn_orient_matrix_UB_21      -0.0004457000
_diffrn_orient_matrix_UB_22      0.0009689000
_diffrn_orient_matrix_UB_23      0.0013202000
_diffrn_orient_matrix_UB_31      0.0005851000
_diffrn_orient_matrix_UB_32      0.0007715000
_diffrn_orient_matrix_UB_33      -0.0016506000
_diffrn_radiation_probe          electron
_diffrn_radiation_type           '200 keV electrons'
_diffrn_radiation_wavelength     0.0251
_diffrn_reflns_av_R_equivalents  0.1965
_diffrn_reflns_av_unetI/netI     0.1603
_diffrn_reflns_Laue_measured_fraction_full 0.803
_diffrn_reflns_Laue_measured_fraction_max 0.803
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       20
_diffrn_reflns_limit_k_min       -20
_diffrn_reflns_limit_l_max       11
_diffrn_reflns_limit_l_min       -11
_diffrn_reflns_number            3064
_diffrn_reflns_point_group_measured_fraction_full 0.810
_diffrn_reflns_point_group_measured_fraction_max 0.810
_diffrn_reflns_theta_full        0.719
_diffrn_reflns_theta_max         0.719
_diffrn_reflns_theta_min         0.117
_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  0.58108
_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    1.120
_exptl_crystal_description       block
_exptl_crystal_F_000             279
_exptl_crystal_size_max          0.0004
_exptl_crystal_size_mid          0.0002
_exptl_crystal_size_min          0.0002
_refine_diff_density_max         0.084
_refine_diff_density_min         -0.108
_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       520(79)
_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   1.031
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     218
_refine_ls_number_reflns         1543
_refine_ls_number_restraints     289
_refine_ls_restrained_S_all      0.958
_refine_ls_R_factor_all          0.1722
_refine_ls_R_factor_gt           0.1067
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1721P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2658
_refine_ls_wR_factor_ref         0.3098
_reflns_Friedel_coverage         0.898
_reflns_Friedel_fraction_full    0.819
_reflns_Friedel_fraction_max     0.819
_reflns_number_gt                837
_reflns_number_total             1543
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1ce01172c1.cif
_cod_data_source_block           exp_502
_cod_depositor_comments
'Adding full bibliography for 7243939--7243951.cif.'
_cod_original_cell_volume        1822(113)
_cod_database_code               7243943
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C24 H18'
_chemical_oxdiff_usercomment     SA3
_reflns_odcompleteness_completeness 80.90
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     0.72
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
2. Uiso/Uaniso restraints and constraints
C011 \\sim C012 \\sim C014 \\sim C017 \\sim C021 \\sim C023: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
C003 \\sim C008 \\sim C019 \\sim C020 \\sim C022 \\sim C025: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
C009 \\sim C010 \\sim C013 \\sim C015 \\sim C016 \\sim C018: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
C005 \\sim C002 \\sim C007 \\sim C001 \\sim C006 \\sim C004: within 2A with
sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
3. Rigid body (RIGU) restrains
 C017, C012, C023, C011, C021, C014
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C009, C010, C013, C015, C016, C018
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C005, C002, C007, C001, C006, C004
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C025, C008, C003, C019, C020, C022
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
4.a Aromatic/amide H refined with riding coordinates:
 C003(H003), C005(H005), C006(H006), C007(H007), C009(H009), C011(H011),
 C012(H012), C013(H013), C014(H014), C015(H015), C016(H016), C018(H018),
 C019(H019), C020(H020), C021(H021), C022(H022), C023(H023), C025(H025)
;
_shelx_res_checksum              27587
_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 1.556
_oxdiff_exptl_absorpt_empirical_full_min 0.814