Cytotoxic Kendomycins Containing the Carbacylic <i>Ansa</i> Scaffold from the Marine-Derived <i>Verrucosispora</i> sp. SCSIO 07399.
Zhang, Shanwen; Xie, Qing; Sun, Changli; Tian, Xin-Peng; Gui, Chun; Qin, Xiangjing; Zhang, Hua; Ju, Jianhua; Journal of natural products  (2019) –; doi:10.1021/acs.jnatprod.9b00654

data_1556260
_publ_section_title
;
 Cytotoxic Kendomycins Containing the Carbacylic <i>Ansa</i> Scaffold from
 the Marine-Derived <i>Verrucosispora</i> sp. SCSIO 07399.
;
_journal_name_full               'Journal of natural products'
_journal_paper_doi               10.1021/acs.jnatprod.9b00654
_journal_year                    2019
_chemical_absolute_configuration 5R,6R,7S,8R,9R,12S,16S,18S,19S
_chemical_formula_moiety         'C28 H40 O6'
_chemical_formula_sum            'C28 H40 O6'
_chemical_formula_weight         472.60
_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     iterative
_audit_creation_date             2019-10-09
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   10.5277(3)
_cell_length_b                   18.7745(6)
_cell_length_c                   16.6567(7)
_cell_measurement_reflns_used    8339
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      73.2440
_cell_measurement_theta_min      4.9580
_cell_volume                     3292.2(2)
_computing_cell_refinement       'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_computing_data_collection       'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_computing_data_reduction        'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_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_environment      N~2~
_diffrn_ambient_temperature      100.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.982
_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    -20.00  21.00   0.50    9.93    --    0.00 -82.00 150.00   82
  2  \w    -32.00  30.00   0.50    9.93    --    0.00 -82.00 -30.00  124
  3  \w    -30.00  29.00   0.50    9.93    --    0.00 -82.00  90.00  118
  4  \w      8.00  46.00   0.50   48.71    --   94.60 -30.00 -30.00   76
  5  \w     10.00 108.00   0.50   48.71    --   94.60 -61.00 -60.00  196
  6  \w     77.00 122.00   0.50   48.71    --   94.60  15.00  60.00   90
  7  \w    149.00 179.00   0.50   48.71    --   94.60  15.00  60.00   60
  8  \w     52.00  96.00   0.50   48.71    --   94.60 -30.00 -30.00   88
  9  \w     79.00 106.00   0.50   48.71    --   94.60 -45.00 -30.00   54
 10  \w     25.00 120.00   0.50   48.71    --   94.60 -77.00 -60.00  190
 11  \w      6.00 179.00   0.50   48.71    --   94.60   0.00-120.00  346
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC12 (RINC): Kappa single'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.1236758000
_diffrn_orient_matrix_UB_12      0.0258481000
_diffrn_orient_matrix_UB_13      0.0398731000
_diffrn_orient_matrix_UB_21      0.0652653000
_diffrn_orient_matrix_UB_22      0.0024092000
_diffrn_orient_matrix_UB_23      -0.0827825000
_diffrn_orient_matrix_UB_31      -0.0429448000
_diffrn_orient_matrix_UB_32      0.0778513000
_diffrn_orient_matrix_UB_33      -0.0107690000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0369
_diffrn_reflns_av_unetI/netI     0.0395
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.982
_diffrn_reflns_limit_h_max       12
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -16
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            17566
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.966
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.837
_diffrn_reflns_theta_min         4.711
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.531
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.81056
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.33c (Rigaku Oxford Diffraction, 2017)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear whiteish white'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   whiteish
_exptl_crystal_colour_primary    white
_exptl_crystal_density_diffrn    0.953
_exptl_crystal_description       plate
_exptl_crystal_F_000             1024
_exptl_crystal_size_max          0.2
_exptl_crystal_size_mid          0.05
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.299
_refine_diff_density_min         -0.218
_refine_diff_density_rms         0.054
_refine_ls_abs_structure_details
;
 Flack x determined using 1924 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.04(11)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.086
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     316
_refine_ls_number_reflns         6458
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.086
_refine_ls_R_factor_all          0.0703
_refine_ls_R_factor_gt           0.0593
_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^)+(0.1083P)^2^+0.3136P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1683
_refine_ls_wR_factor_ref         0.1776
_reflns_Friedel_coverage         0.753
_reflns_Friedel_fraction_full    0.998
_reflns_Friedel_fraction_max     0.946
_reflns_number_gt                5221
_reflns_number_total             6458
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            np9b00654_si_002.cif
_cod_data_source_block           zhangshanwen_f8-399_collect
_cod_depositor_comments
;

2022-09-17
Z value and formula fixed to values more according to usual
chemical conventions.                 miguel
;
_cod_original_formula_sum            'C112 H160 O24'
_cod_original_formula_weight         1890.39
_cod_original_formula_moiety         '4(C28 H40 O6)'
_cod_original_formula_units_Z            1
_cod_original_cell_volume        3292.24(18)
_cod_database_code               1556260
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         'C116 H152 O32 '
_shelx_estimated_absorpt_t_max   0.989
_shelx_estimated_absorpt_t_min   0.901
_reflns_odcompleteness_completeness 99.91
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_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.a Ternary CH refined with riding coordinates:
 C8(H8), C5(H5A), C9(H9), C6(H6), C7(H7), C18(H18), C16(H16), C12(H12)
2.b Secondary CH2 refined with riding coordinates:
 C10(H10A,H10B), C17(H17A,H17B), C11(H11A,H11B), C15(H15A,H15B)
2.c Aromatic/amide H refined with riding coordinates:
 C2(H2A), C20(H20), C13(H13)
2.d Idealised Me refined as rotating group:
 C22(H22A,H22B,H22C), C21(H21A,H21B,H21C), C26(H26A,H26B,H26C), C25(H25A,H25B,
 H25C), C23(H23A,H23B,H23C), C24(H24A,H24B,H24C)
2.e Idealised tetrahedral OH refined as rotating group:
 O5(H5), O4(H4), O2(H2)
;
_shelx_res_checksum              34613
_shelx_hkl_checksum              47207
_shelx_fab_checksum              17388
_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 1.689
_oxdiff_exptl_absorpt_empirical_full_min 0.486