Absolute configuration determination of SMTP-7 via microcrystal electron diffraction (MicroED)
Wang, Bo; Lin, Yiqing; Chemical Communications  (2022) –; doi:10.1039/D2CC05218K

data_7130937
_publ_section_title
;
 Absolute configuration determination of SMTP-7 via microcrystal electron
 diffraction (MicroED)
;
_journal_name_full               'Chemical Communications'
_journal_paper_doi               10.1039/D2CC05218K
_journal_year                    2022
_chemical_absolute_configuration unk
_chemical_formula_moiety         'C51 H68 N2 O10'
_chemical_formula_sum            'C51 H68 N2 O10'
_chemical_formula_weight         869.11
_chemical_name_common            SMTP-7D
_chemical_name_systematic
'(S)-2,5-bis((2R,3S)-2-((E)-4,8-dimethylnona-3,7-dien-1-yl)-3,5-dihydroxy-2-methyl-7-oxo-3,4,7,9-tetrahydropyrano[2,3-e]isoindol-8(2H)-yl)pentanoic acid'
_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             2022-09-12
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6408)
;
_audit_update_record
;
2022-09-20 deposited with the CCDC.	2022-10-14 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   11.238(2)
_cell_length_b                   13.188(3)
_cell_length_c                   30.929(6)
_cell_measurement_reflns_used    40819
_cell_measurement_temperature    80.15
_cell_measurement_theta_max      0.716
_cell_measurement_theta_min      0.059
_cell_volume                     4583.9(16)
_computing_cell_refinement       'dials.cosym (Gildea, et al., 2018)'
_computing_data_collection       'Leginon (Cheng et al., 2021)'
_computing_data_reduction        'DIALS (Clabbers et al., 2018)'
_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      80.15
_diffrn_detector                 CMOS
_diffrn_detector_area_resol_mean 35.7
_diffrn_detector_type            'Thermo Fisher CETA-D'
_diffrn_measured_fraction_theta_full 0.810
_diffrn_measured_fraction_theta_max 0.810
_diffrn_measurement_device       'transmission electron microscope'
_diffrn_measurement_device_type  'Thermo Fisher Glacios at 200keV'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_probe          electron
_diffrn_radiation_type           electron
_diffrn_radiation_wavelength     0.02501
_diffrn_reflns_av_R_equivalents  0.1908
_diffrn_reflns_av_unetI/netI     0.1136
_diffrn_reflns_Laue_measured_fraction_full 0.810
_diffrn_reflns_Laue_measured_fraction_max 0.810
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       26
_diffrn_reflns_limit_l_min       -27
_diffrn_reflns_number            40819
_diffrn_reflns_point_group_measured_fraction_full 0.826
_diffrn_reflns_point_group_measured_fraction_max 0.826
_diffrn_reflns_theta_full        0.716
_diffrn_reflns_theta_max         0.716
_diffrn_reflns_theta_min         0.059
_diffrn_source                   'transmission electron microscope'
_diffrn_source_type              'Thermo Fisher Glacios at 200keV'
_diffrn_source_voltage           200
_exptl_absorpt_coefficient_mu    0.000
_exptl_absorpt_correction_type   none
_exptl_absorpt_process_details   'electron diffraction, unknown absorption'
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.259
_exptl_crystal_description       'fine powder'
_exptl_crystal_F_000             727
_refine_diff_density_max         0.105
_refine_diff_density_min         -0.123
_refine_diff_density_rms         0.035
_refine_ls_abs_structure_details
;
 All f" are zero, so absolute structure could not be determined
;
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.206
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     581
_refine_ls_number_reflns         3965
_refine_ls_number_restraints     408
_refine_ls_restrained_S_all      1.165
_refine_ls_R_factor_all          0.1880
_refine_ls_R_factor_gt           0.1454
_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^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3458
_refine_ls_wR_factor_ref         0.3675
_reflns_Friedel_coverage         0.785
_reflns_Friedel_fraction_full    0.847
_reflns_Friedel_fraction_max     0.847
_reflns_number_gt                2303
_reflns_number_total             3965
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2cc05218k2.cif
_cod_data_source_block           540p6s1_z4_p212121_3
_cod_original_cell_volume        4584.2(16)
_cod_database_code               7130937
_shelx_shelxl_version_number     2018/3
_exptl_absorpt_special_details   dials.scale
_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 C(H,H,H) groups, All O(H) groups
2. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 2A with sigma of 0.005 and sigma
for terminal atoms of 0.005 within 2A
3.a Ternary CH refined with riding coordinates:
 C8A(H8A), C1C(H1C), C8B(H8B)
3.b Secondary CH2 refined with riding coordinates:
 C19A(H19A,H19B), C18A(H18A,H18B), C15A(H15A,H15B), C14A(H14D,H14E), C7A(H7AA,
 H7AB), C13A(H13A,H13B), C2C(H2CA,H2CB), C3C(H3CA,H3CB), C4C(H4CA,H4CB),
 C13B(H13C,H13D), C7B(H7BA,H7BB), C14B(H14F,H14G), C15B(H15C,H15D), C18B(H18C,
 H18D), C19B(H19C,H19D)
3.c Aromatic/amide H refined with riding coordinates:
 C20A(H20A), C16A(H16A), C4A(H4A), C4B(H4B), C16B(H16B), C20B(H20B)
3.d Idealised Me refined as rotating group:
 C23A(H23A,H23B,H23C), C22A(H22A,H22B,H22C), C14(H14A,H14B,H14C), C24A(H24A,
 H24B,H24C), C25B(H25B,H25C,H25D), C24B(H24D,H24E,H24F), C23B(H23D,H23E,H23F),
 C22B(H22D,H22E,H22F)
3.e Idealised tetrahedral OH refined as rotating group:
 O25A(H25A), O26A(H26A), O7C(H7C), O27B(H27B), O26B(H26B)
;
_shelx_res_checksum              50177
_shelx_hkl_checksum              29297
_olex2_submission_special_instructions 'No special instructions were received'