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

data_7130936
_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-7, TMS007, BIIB131'
_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           18
_space_group_name_Hall           'P 2 2ab'
_space_group_name_H-M_alt        'P 21 21 2'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2022-09-07
_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                   12.897(3)
_cell_length_b                   31.766(6)
_cell_length_c                   11.213(2)
_cell_measurement_reflns_used    161403
_cell_measurement_temperature    80.15
_cell_measurement_theta_max      0.799
_cell_measurement_theta_min      0.06
_cell_volume                     4593.8(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 0.842
_diffrn_measured_fraction_theta_max 0.842
_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  0.3779
_diffrn_reflns_av_unetI/netI     0.3929
_diffrn_reflns_Laue_measured_fraction_full 0.842
_diffrn_reflns_Laue_measured_fraction_max 0.842
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -14
_diffrn_reflns_limit_k_max       29
_diffrn_reflns_limit_k_min       -31
_diffrn_reflns_limit_l_max       12
_diffrn_reflns_limit_l_min       -12
_diffrn_reflns_number            161403
_diffrn_reflns_point_group_measured_fraction_full 0.855
_diffrn_reflns_point_group_measured_fraction_max 0.855
_diffrn_reflns_theta_full        0.799
_diffrn_reflns_theta_max         0.799
_diffrn_reflns_theta_min         0.060
_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    1.257
_exptl_crystal_description       'fine powder'
_exptl_crystal_F_000             752
_refine_diff_density_max         0.180
_refine_diff_density_min         -0.263
_refine_diff_density_rms         0.048
_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   0.984
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     437
_refine_ls_number_reflns         5710
_refine_ls_number_restraints     614
_refine_ls_restrained_S_all      1.006
_refine_ls_R_factor_all          0.2661
_refine_ls_R_factor_gt           0.1619
_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          0.3786
_refine_ls_wR_factor_ref         0.4095
_reflns_Friedel_coverage         0.798
_reflns_Friedel_fraction_full    0.872
_reflns_Friedel_fraction_max     0.872
_reflns_number_gt                1666
_reflns_number_total             5710
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2cc05218k2.cif
_cod_data_source_block           540_p1_s1_P21_t2_2x_P21212_bo7_submit
_cod_database_code               7130936
_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, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Restrained distances
 C9B-C24B \\sim C9B-C14B \\sim C14B-C15B \\sim C14B-C1 \\sim C15B-C16B \\sim
C1-C16B \\sim C17B-C25B ~
 C2-C3 \\sim C17B-C18B \\sim C2-C18B \\sim C18B-C19B \\sim C19B-C20B \\sim
C21B-C23B \\sim C21B-C22B
 with sigma of 0.02
 C14B-C16B \\sim C18B-C20B \\sim C14A-C16A \\sim C18A-C20A
 with sigma of 0.02
 C16B-C17B \\sim C20B-C21B \\sim C16A-C17A \\sim C20A-C21A
 with sigma of 0.02
 C9A-C25A \\sim C9A-C14A \\sim C14A-C15A \\sim C15A-C16A \\sim C17A-C24A \\sim
C17A-C18A \\sim C18A-
 C19A \\sim C19A-C20A \\sim C21A-C22A \\sim C21A-C23A
 with sigma of 0.02
 C16A-C24A \\sim C16A-C18A \\sim C16B-C25B \\sim C16B-C3 \\sim C16B-C18B
 with sigma of 0.02
 C20A-C22A \\sim C20A-C23A
 with sigma of 0.02
3. Restrained planarity
 C16B, C18B, C17B, C25B
 with sigma of 0.1
 C16B, C18B, C2, C3
 with sigma of 0.1
 C16A, C17A, C18A, C24A
 with sigma of 0.1
 C20A, C21A, C22A, C23A
 with sigma of 0.1
 C20B, C21B, C22B, C23B
 with sigma of 0.1
4. 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
Uanis(C25A) = Uanis(C14A) = Uanis(C15A) = Uanis(C16A) = Uanis(C17A) =
Uanis(C24A) = Uanis(C18A) = Uanis(C19A) = Uanis(C20A) = Uanis(C21A) =
Uanis(C22A) = Uanis(C23A)
Uanis(C24B) = Uanis(C14B) = Uanis(C15B) = Uanis(C16B) = Uanis(C17B) =
Uanis(C25B) = Uanis(C18B) = Uanis(C19B) = Uanis(C20B) = Uanis(C21B) =
Uanis(C23B) = Uanis(C22B) = Uanis(C1) = Uanis(C3) = Uanis(C2)
Uanis(C1C) = Uanis(C2C) = Uanis(C3C) = Uanis(C4C) = Uanis(C5C)
5. Others
 Sof(H14C)=Sof(H14D)=Sof(H16B)=Sof(H18C)=Sof(H18D)=Sof(C1)=Sof(H1A)=Sof(H1B)=
 Sof(C2)=Sof(C3)=Sof(H3A)=Sof(H3B)=Sof(H3C)=1-FVAR(1)
 Sof(H14E)=Sof(H14F)=Sof(H16C)=Sof(H18E)=Sof(H18F)=Sof(C15B)=Sof(H15C)=
 Sof(H15D)=Sof(C17B)=Sof(C25B)=Sof(H25D)=Sof(H25E)=Sof(H25F)=FVAR(1)
6.a Ternary CH refined with riding coordinates:
 C1C(H1C), C8A(H8A), C8B(H8B)
6.b Secondary CH2 refined with riding coordinates:
 C2C(H2CA,H2CB), C3C(H3CA,H3CB), C4C(H4CA,H4CB), C7A(H7AA,H7AB), C7B(H7BA,
 H7BB), C13A(H13A,H13B), C13B(H13C,H13D), C14A(H14A,H14B), C14B(H14C,H14D),
 C14B(H14E,H14F), C15A(H15A,H15B), C18A(H18A,H18B), C18B(H18E,H18F), C18B(H18C,
 H18D), C19A(H19A,H19B), C19B(H19C,H19D), C15B(H15C,H15D), C1(H1A,H1B)
6.c Aromatic/amide H refined with riding coordinates:
 C4A(H4A), C4B(H4B), C16A(H16A), C16B(H16C), C16B(H16B), C20A(H20A), C20B(H20B)
6.d Idealised Me refined as rotating group:
 C22A(H22A,H22B,H22C), C22B(H22D,H22E,H22F), C23A(H23A,H23B,H23C), C23B(H23D,
 H23E,H23F), C24A(H24A,H24B,H24C), C24B(H24D,H24E,H24F), C25A(H25A,H25B,H25C),
 C25B(H25D,H25E,H25F), C3(H3A,H3B,H3C)
6.e Idealised tetrahedral OH refined as rotating group:
 O8C(H8C), O26A(H26A), O26B(H26B), O27A(H27A), O27B(H27B)
;
_shelx_res_checksum              68007
_shelx_hkl_checksum              15058
_olex2_submission_special_instructions 'No special instructions were received'