Antitubercular Ilamycins from Marine-Derived Streptomyces atratus SCSIO ZH16 ΔilaR
Sun, Changli; Liu, Zhiyong; Zhu, Xiangcheng; Fan, Zhiying; Huang, Xuanmei; Wu, Qiaoling; Zheng, Xiaohong; Qin, Xiangjing; Zhang, Tianyu; Zhang, Hua; Ju, Jianhua; Ma, Junying; Journal of Natural Products  (2020) –; doi:10.1021/acs.jnatprod.0c00151

data_1557882
_publ_section_title
;
 Antitubercular Ilamycins from Marine-Derived Streptomyces atratus SCSIO
 ZH16 \DilaR
;
_journal_name_full               'Journal of Natural Products'
_journal_paper_doi               10.1021/acs.jnatprod.0c00151
_journal_year                    2020
_chemical_absolute_configuration rm
_chemical_formula_moiety         'C54 H75 N9 O13'
_chemical_formula_sum            'C54 H75 N9 O13'
_chemical_formula_weight         1058.23
_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   mixed
_audit_creation_date             2020-02-08
_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                   31.3214(9)
_cell_length_b                   17.9026(7)
_cell_length_c                   12.6750(6)
_cell_measurement_reflns_used    10911
_cell_measurement_temperature    100(6)
_cell_measurement_theta_max      72.0380
_cell_measurement_theta_min      3.7450
_cell_volume                     7107.3(5)
_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    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100(6)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.999
_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    105.00 135.00   0.30    6.59    --   45.70  82.00 -90.00  100
  2  \w     87.00 135.00   0.30    6.59    --   45.70  82.00  90.00  160
  3  \w    100.00 134.20   0.30    6.59    --   45.70  57.00 -60.00  114
  4  \w     23.00  92.30   0.30    6.59    --   45.70  57.00 -60.00  231
  5  \w     85.00 126.10   0.30    6.59    --   45.70  77.00   0.00  137
  6  \w     87.00 121.20   0.30    6.59    --   45.70  82.00  60.00  114
  7  \w     84.00 130.20   0.30    6.59    --   45.70  77.00-120.00  154
  8  \w     18.00 125.40   0.30   26.35    --  100.10 -82.00 -30.00  358
  9  \w     76.00 170.20   0.30   26.35    --  100.10  61.00 -30.00  314
 10  \w     36.00  79.20   0.30   26.35    --  100.10 -61.00   0.00  144
 11  \w     87.00 175.20   0.30   26.35    --  100.10  61.00 150.00  294
 12  \w     73.00 186.40   0.30   26.35    --  100.10  61.00 -90.00  378
 13  \w    105.00 131.10   0.30   26.35    --  100.10 -61.00   0.00   87
 14  \w     72.00 181.20   0.30   26.35    --  100.10  61.00-150.00  364
;
_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      -0.0268071000
_diffrn_orient_matrix_UB_12      0.0456464000
_diffrn_orient_matrix_UB_13      -0.0789746000
_diffrn_orient_matrix_UB_21      -0.0412609000
_diffrn_orient_matrix_UB_22      -0.0301204000
_diffrn_orient_matrix_UB_23      0.0508640000
_diffrn_orient_matrix_UB_31      -0.0002723000
_diffrn_orient_matrix_UB_32      0.0665882000
_diffrn_orient_matrix_UB_33      0.0768027000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0651
_diffrn_reflns_av_unetI/netI     0.0677
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       29
_diffrn_reflns_limit_h_min       -37
_diffrn_reflns_limit_k_max       21
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            34009
_diffrn_reflns_point_group_measured_fraction_full 0.989
_diffrn_reflns_point_group_measured_fraction_max 0.989
_diffrn_reflns_theta_full        67.080
_diffrn_reflns_theta_max         67.080
_diffrn_reflns_theta_min         3.487
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.586
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.09811
_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 light yellow'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    0.989
_exptl_crystal_description       plate
_exptl_crystal_F_000             2264
_exptl_crystal_size_max          0.1
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.05
_platon_squeeze_details
;
TITL sunchangliP 21 21 2llecR = 0.18
CELL   31.3214   17.9026   12.6750     90.00     90.00     90.00
SPGR P21212
Q101 0.263 0.440 0.187 !       7.27 eA-3
C102 0.121 0.471 0.421 !       6.90 eA-3
C103 0.555 0.528 0.397 !       5.67 eA-3
C104 0.013 0.965 0.738 !       4.72 eA-3
C105 0.757 0.059 0.927 !       4.71 eA-3
C106 0.500 0.501 0.563 !       3.75 eA-3
Q107 0.032 0.050 0.533 !       3.43 eA-3
Q108 0.936 0.375 0.921 !       3.14 eA-3
C109 0.542 0.096 0.513 !       3.12 eA-3
C110 0.100 0.467 0.158 !       2.62 eA-3
C111 1.000 0.997 0.593 !       2.59 eA-3
C112 0.012 0.640 0.291 !       2.25 eA-3
C113 0.469 0.895 0.082 !       2.04 eA-3
C114 0.857 0.464 0.921 !       1.79 eA-3
C115 0.866 0.484 0.887 !       1.75 eA-3
C116 0.383 0.031 0.011 !       1.71 eA-3
C117 0.861 0.503 0.127 !       1.60 eA-3
C118 0.031 1.001 0.656 !       1.56 eA-3
C119 1.000 0.497 0.611 !       1.54 eA-3
C120 0.018 0.578 0.064 !       1.42 eA-3
C121 0.940 0.562 0.101 !       1.32 eA-3
C122 0.516 0.060 0.760 !       1.31 eA-3
C123 0.024 0.425 0.142 !       1.30 eA-3
Q124 0.970 0.658 0.612 !       1.29 eA-3
C125 0.523 0.098 0.776 !       1.28 eA-3
C126 0.416 0.996 0.313 !       1.22 eA-3
C127 0.984 0.402 0.985 !       1.20 eA-3
C128 0.466 0.903 0.854 !       1.16 eA-3
C129 0.446 0.984 0.258 !       1.11 eA-3
C130 0.950 0.585 0.595 !       1.09 eA-3
C131 0.443 0.950 0.299 !       1.08 eA-3
C132 0.111 0.567 0.794 !       1.03 eA-3
C133 0.071 0.437 0.599 !       0.97 eA-3
C134 0.541 0.065 0.375 !       0.94 eA-3
C135 0.397 0.980 0.919 !       0.82 eA-3
C136 0.526 0.079 0.982 !       0.82 eA-3
C137 0.056 0.520 0.638 !       0.81 eA-3
Q138 0.482 0.863 0.317 !       0.76 eA-3
C139 0.468 0.961 0.456 !       0.75 eA-3
C140 0.440 0.923 0.196 !       0.75 eA-3
C141 0.530 0.050 0.204 !       0.75 eA-3
C142 0.502 0.059 0.157 !       0.74 eA-3
C143 0.086 0.464 0.842 !       0.73 eA-3
C144 0.406 0.019 0.228 !       0.72 eA-3
C145 0.096 0.543 0.899 !       0.70 eA-3
C146 0.252 0.875 0.981 !       0.68 eA-3
Q147 0.046 0.917 0.665 !       0.68 eA-3
Q148 0.930 0.359 0.024 !       0.68 eA-3
C149 0.961 0.493 0.656 !       0.66 eA-3
C150 0.344 1.003 0.962 !       0.66 eA-3
C151 0.506 0.965 0.708 !       0.66 eA-3
Q152 0.385 0.047 0.716 !       0.66 eA-3
C153 0.008 0.435 0.626 !       0.64 eA-3
C154 0.491 0.969 0.147 !       0.64 eA-3
Q155 0.310 0.145 0.064 !       0.62 eA-3
Q156 0.420 0.073 0.196 !       0.60 eA-3
Q157 0.233 0.513 0.116 !       0.60 eA-3
Q158 0.947 0.425 0.846 !       0.59 eA-3
Q159 0.600 0.828 0.124 !       0.59 eA-3
C160 0.242 0.532 0.086 !       0.58 eA-3
C161 0.137 0.541 0.081 !       0.58 eA-3
C162 0.031 0.550 0.587 !       0.57 eA-3
C163 0.133 0.641 0.890 !       0.57 eA-3
C164 0.460 0.891 0.947 !       0.57 eA-3
C165 0.011 0.513 0.078 !       0.56 eA-3
Q166 0.623 0.016 0.454 !       0.56 eA-3
Q167 0.470 0.186 0.802 !       0.55 eA-3
Q168 0.107 0.486 0.622 !       0.54 eA-3
C169 0.919 0.485 0.851 !       0.53 eA-3
C170 0.032 0.518 0.561 !       0.52 eA-3
C171 0.414 0.997 0.449 !       0.52 eA-3
C172 0.482 0.985 0.052 !       0.52 eA-3
C173 0.916 0.567 0.851 !       0.52 eA-3
Q174 0.384 0.012 0.468 !       0.51 eA-3
Q175 0.615 0.036 0.422 !       0.50 eA-3
;
_refine_diff_density_max         0.438
_refine_diff_density_min         -0.267
_refine_diff_density_rms         0.045
_refine_ls_abs_structure_details
;
 Flack x determined using 3186 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.83(11)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.026
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     697
_refine_ls_number_reflns         12559
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.026
_refine_ls_R_factor_all          0.0796
_refine_ls_R_factor_gt           0.0576
_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^)+(0.1089P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1587
_refine_ls_wR_factor_ref         0.1727
_reflns_Friedel_coverage         0.794
_reflns_Friedel_fraction_full    0.975
_reflns_Friedel_fraction_max     0.975
_reflns_number_gt                9247
_reflns_number_total             12559
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            np0c00151_si_003.cif
_cod_data_source_block           sunchangli_il-5b_collect_sq
_cod_database_code               1557882
_shelx_shelxl_version_number     2016/6
_shelx_estimated_absorpt_t_max   0.971
_shelx_estimated_absorpt_t_min   0.944
_reflns_odcompleteness_completeness 99.90
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, H47 of O47, {H64A,H64B,H64C} of C64, All C(H,H) groups,
  All N(H) groups
 At 1.5 times of:
  H54 of O54, {H36A,H36B,H36C} of C36, {H35A,H35B,H35C} of C35, {H72A,H72B,
  H72C} of C72, {H3AA,H3AB,H3AC} of C3AA, {H65A,H65B,H65C} of C65, H52 of O52,
  {H74A,H74B,H74C} of C74, {H69A,H69B,H69C} of C69, {H73A,H73B,H73C} of C73,
  {H75A,H75B,H75C} of C75
2.a Rotating group:
 O47(H47)
2.b Ternary CH refined with riding coordinates:
 C2AA(H2AA), C13(H13), C19(H19), C16(H16), C7(H7), C1AA(H1AA), C10(H10),
 C71(H71), C63(H63), C49(H49)
2.c Secondary CH2 refined with riding coordinates:
 C22(H22A,H22B), C66(H66A,H66B), C37(H37A,H37B), C70(H70A,H70B), C48(H48A,
 H48B), C62(H62A,H62B), C53(H53A,H53B)
2.d Aromatic/amide H refined with riding coordinates:
 N2(H2), N14(H14), N5(H5), N8(H8), N17(H17), C24(H24), C27(H27), C30(H30),
 C29(H29), C39(H39), C43(H43), C40(H40), C33(H33), C68(H68), C67(H67), C28(H28)
2.e Tetrahedral OH refined with riding coordinates:
 O52(H52)
2.f X=CH2 refined with riding coordinates:
 C34(H34A,H34B)
2.g Idealised Me refined as rotating group:
 C65(H65A,H65B,H65C), C75(H75A,H75B,H75C), C74(H74A,H74B,H74C), C69(H69A,H69B,
 H69C), C73(H73A,H73B,H73C), C36(H36A,H36B,H36C), C64(H64A,H64B,H64C), C35(H35A,
 H35B,H35C), C72(H72A,H72B,H72C), C3AA(H3AA,H3AB,H3AC)
2.h Idealised tetrahedral OH refined as rotating group:
 O54(H54)
;
_platon_squeeze_void_probe_radius 1.20
_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 5.891
_oxdiff_exptl_absorpt_empirical_full_min 0.319