Crystal Structure and Physical Stability of Ginsenoside Compound-K Solvates
Chen, Jinyao; Zhu, Wenming; Ji, Weijie; Zhu, Bin; Guo, Chunyang; Qi, Ming-Hui; Ren, Guo-Bin; CrystEngComm  (2019) –; doi:10.1039/C9CE00965E

data_7234740
_publ_section_title
;
 Crystal Structure and Physical Stability of Ginsenoside Compound-K
 Solvates
;
_journal_name_full               CrystEngComm
_journal_paper_doi               10.1039/C9CE00965E
_journal_year                    2019
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C3 H8 O, C36 H62 O8, 2(H2 O)'
_chemical_formula_sum            'C39 H74 O11'
_chemical_formula_weight         718.98
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_symmetry_space_group_name_Hall  'P 2yb'
_symmetry_space_group_name_H-M   'P 1 21 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     iterative
_audit_creation_date             2019-08-19
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2019-08-19 deposited with the CCDC.    2019-10-21 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 95.908(7)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   11.5408(18)
_cell_length_b                   12.3313(17)
_cell_length_c                   14.1447(19)
_cell_measurement_reflns_used    1387
_cell_measurement_temperature    170.21
_cell_measurement_theta_max      66.129
_cell_measurement_theta_min      29.192
_cell_volume                     2002.3(5)
_computing_cell_refinement       'SAINT V8.38A (?, 2016)'
_computing_data_reduction        'SAINT V8.38A (?, 2016)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'olex2.solve (Bourhis et al., 2015)'
_diffrn_ambient_temperature      170.21
_diffrn_measured_fraction_theta_full 0.996
_diffrn_measured_fraction_theta_max 0.996
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0805
_diffrn_reflns_av_unetI/netI     0.0545
_diffrn_reflns_Laue_measured_fraction_full 0.996
_diffrn_reflns_Laue_measured_fraction_max 0.996
_diffrn_reflns_limit_h_max       13
_diffrn_reflns_limit_h_min       -13
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            32854
_diffrn_reflns_point_group_measured_fraction_full 0.991
_diffrn_reflns_point_group_measured_fraction_max 0.991
_diffrn_reflns_theta_full        67.251
_diffrn_reflns_theta_max         67.251
_diffrn_reflns_theta_min         3.141
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.689
_exptl_absorpt_correction_T_max  0.7528
_exptl_absorpt_correction_T_min  0.6274
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'SADABS-2016/2 (Bruker,2016/2) was used for absorption correction. wR2(int) was 0.1350 before and 0.0824 after correction. The Ratio of minimum to maximum transmission is 0.8334. The \l/2 correction factor is Not present.'
_exptl_crystal_colour            white
_exptl_crystal_colour_primary    white
_exptl_crystal_density_diffrn    1.193
_exptl_crystal_description       plate
_exptl_crystal_F_000             792
_exptl_crystal_size_max          0.19
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.06
_refine_diff_density_max         0.157
_refine_diff_density_min         -0.159
_refine_diff_density_rms         0.035
_refine_ls_abs_structure_details
;
 Flack x determined using 2409 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.02(13)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.072
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     529
_refine_ls_number_reflns         7103
_refine_ls_number_restraints     84
_refine_ls_restrained_S_all      1.078
_refine_ls_R_factor_all          0.0517
_refine_ls_R_factor_gt           0.0430
_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^)+(0.0296P)^2^+0.2590P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0905
_refine_ls_wR_factor_ref         0.0952
_reflns_Friedel_coverage         0.895
_reflns_Friedel_fraction_full    0.986
_reflns_Friedel_fraction_max     0.986
_reflns_number_gt                6178
_reflns_number_total             7103
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c9ce00965e2.cif
_cod_data_source_block           sc263_183_32_13_0m_a
_cod_database_code               7234740
_shelx_shelxl_version_number     2014/7
_shelx_estimated_absorpt_t_max   0.960
_shelx_estimated_absorpt_t_min   0.880
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, {H37A,H37B,H37C} of C37, All C(H,H) groups
 At 1.5 times of:
  All O(H) groups, {H39D,H39E,H39F} of C39A, {H37D,H37E,H37F} of C37A, {H39A,
  H39B,H39C} of C39, {H18A,H18B,H18C} of C18, {H21A,H21B,H21C} of C21, {H19A,
  H19B,H19C} of C19, {H27A,H27B,H27C} of C27, {H26A,H26B,H26C} of C26, {H28A,
  H28B,H28C} of C28, {H30A,H30B,H30C} of C30, {H29A,H29B,H29C} of C29
2. Restrained distances
 O9-C38 \\sim O9-C38A
 with sigma of 0.02
 O9-C37 \\sim O9-C39
 with sigma of 0.02
 C38-C37 \\sim C38-C39
 with sigma of 0.02
3. Rigid bond restraints
 C37, C38, C39, C37A, C38A, C39A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
C37 \\sim C38 \\sim C39 \\sim C37A \\sim C38A \\sim C39A: within 2A with sigma
of 0.01 and sigma for terminal atoms of 0.02
5. Same fragment restrains
{O9, C37A, C38A, C39A} sigma for 1-2: 0.02, 1-3: 0.04
as
{O9, C37, C38, C39}
6. Others
 Sof(C37A)=Sof(H37D)=Sof(H37E)=Sof(H37F)=Sof(C38A)=Sof(H38A)=Sof(C39A)=
 Sof(H39D)=Sof(H39E)=Sof(H39F)=1-FVAR(1)
 Sof(C37)=Sof(H37A)=Sof(H37B)=Sof(H37C)=Sof(C38)=Sof(H38)=Sof(C39)=Sof(H39A)=
 Sof(H39B)=Sof(H39C)=FVAR(1)
7.a Ternary CH refined with riding coordinates:
 C38(H38), C38A(H38A), C3(H3), C5(H5A), C9(H9), C12(H12), C13(H13), C17(H17),
 C31(H31), C32(H32), C33(H33), C34(H34), C35(H35)
7.b Secondary CH2 refined with riding coordinates:
 C1(H1A,H1B), C2(H2A,H2B), C6(H6A,H6B), C7(H7A,H7B), C11(H11A,H11B), C15(H15A,
 H15B), C16(H16A,H16B), C22(H22A,H22B), C23(H23A,H23B), C36(H36A,H36B)
7.c Aromatic/amide H refined with riding coordinates:
 C24(H24)
7.d Idealised Me refined as rotating group:
 C37(H37A,H37B,H37C), C39(H39A,H39B,H39C), C37A(H37D,H37E,H37F), C39A(H39D,
 H39E,H39F), C18(H18A,H18B,H18C), C19(H19A,H19B,H19C), C21(H21A,H21B,H21C),
 C26(H26A,H26B,H26C), C27(H27A,H27B,H27C), C28(H28A,H28B,H28C), C29(H29A,H29B,
 H29C), C30(H30A,H30B,H30C)
7.e Idealised tetrahedral OH refined as rotating group with stretchable bonds:
 O2(H2), O5(H5), O8(H8)
;
_olex2_submission_special_instructions 'No special instructions were received'