Genome-Guided Discovery of Highly Oxygenated Aromatic Polyketides, Saccharothrixins D-M, from the Rare Marine Actinomycete <i>Saccharothrix</i> sp. D09.
Shen, Qiyao; Dai, Guangzhi; Li, Aiying; Liu, Yang; Zhong, Guannan; Li, Xiaoju; Ren, Xiangmei; Sui, Haiyan; Fu, Jun; Jiao, Nianzhi; Zhang, Youming; Bian, Xiaoying; Zhou, Haibo; Journal of natural products 84 (2021) 2875–2884; doi:10.1021/acs.jnatprod.1c00617

data_1565518
_publ_section_title
;
 Genome-Guided Discovery of Highly Oxygenated Aromatic Polyketides,
 Saccharothrixins D-M, from the Rare Marine Actinomycete
 <i>Saccharothrix</i> sp. D09.
;
_journal_issue                   11
_journal_name_full               'Journal of natural products'
_journal_page_first              2875
_journal_page_last               2884
_journal_paper_doi               10.1021/acs.jnatprod.1c00617
_journal_volume                  84
_journal_year                    2021
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C19 H18 O7, H2 O'
_chemical_formula_sum            'C19 H20 O8'
_chemical_formula_weight         376.35
_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   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2020-07-06
_audit_creation_method
;
Olex2 1.3
(compiled 2020.06.28 svn.raecde09e for OlexSys, GUI svn.r6132)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   9.1402(2)
_cell_length_b                   11.4665(2)
_cell_length_c                   16.0760(3)
_cell_measurement_reflns_used    6445
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      76.0990
_cell_measurement_theta_min      4.7060
_cell_volume                     1684.86(6)
_computing_cell_refinement       'CrysAlisPro 1.171.40.54a (Rigaku OD, 2019)'
_computing_data_collection       'CrysAlisPro 1.171.40.54a (Rigaku OD, 2019)'
_computing_data_reduction        'CrysAlisPro 1.171.40.54a (Rigaku OD, 2019)'
_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    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.995
_diffrn_measured_fraction_theta_max 0.965
_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     34.00 119.00   0.50    0.24    --   45.95  40.00  22.00  170
  2  \w     91.00 177.00   0.50    0.97    --  103.99  40.00  22.00  172
  3  \w     31.00 108.00   0.50    0.97    --  103.99-113.00   8.00  154
  4  \w     31.00 106.00   0.50    0.97    --  103.99 -94.00  60.00  150
  5  \w     31.00 106.00   0.50    0.97    --  103.99 -94.00  30.00  150
  6  \w     18.00  94.00   0.50    0.24    --   45.95-125.00  90.00  152
  7  \w     31.00 108.00   0.50    0.24    --   45.95  57.00-150.00  154
  8  \w   -127.00 -29.00   0.50    0.97    -- -102.00  83.00-150.00  196
  9  \w   -119.00 -74.00   0.50    0.24    --  -45.95-125.00-150.00   90
 10  \w   -119.00 -74.00   0.50    0.24    --  -45.95-125.00 -30.00   90
 11  \w   -119.00 -74.00   0.50    0.24    --  -45.95-125.00  60.00   90
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy R, DW system, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.1270778000
_diffrn_orient_matrix_UB_12      0.0407661000
_diffrn_orient_matrix_UB_13      0.0558226000
_diffrn_orient_matrix_UB_21      -0.0752121000
_diffrn_orient_matrix_UB_22      -0.0558470000
_diffrn_orient_matrix_UB_23      0.0760101000
_diffrn_orient_matrix_UB_31      0.0811742000
_diffrn_orient_matrix_UB_32      -0.1152330000
_diffrn_orient_matrix_UB_33      -0.0170178000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0433
_diffrn_reflns_av_unetI/netI     0.0416
_diffrn_reflns_Laue_measured_fraction_full 0.995
_diffrn_reflns_Laue_measured_fraction_max 0.965
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       10
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       18
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            9100
_diffrn_reflns_point_group_measured_fraction_full 0.951
_diffrn_reflns_point_group_measured_fraction_max 0.897
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         76.311
_diffrn_reflns_theta_min         4.737
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.986
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.32290
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.54a (Rigaku Oxford Diffraction, 2019)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.484
_exptl_crystal_description       block
_exptl_crystal_F_000             792
_exptl_crystal_size_max          0.2
_exptl_crystal_size_mid          0.2
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.184
_refine_diff_density_min         -0.239
_refine_diff_density_rms         0.046
_refine_ls_abs_structure_details
;
 Flack x determined using 1073 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.05(11)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.038
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     252
_refine_ls_number_reflns         3174
_refine_ls_number_restraints     3
_refine_ls_restrained_S_all      1.042
_refine_ls_R_factor_all          0.0409
_refine_ls_R_factor_gt           0.0358
_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^)+(0.0457P)^2^+0.4211P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0860
_refine_ls_wR_factor_ref         0.0888
_reflns_Friedel_coverage         0.619
_reflns_Friedel_fraction_full    0.890
_reflns_Friedel_fraction_max     0.805
_reflns_number_gt                2922
_reflns_number_total             3174
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            np1c00617_si_002.cif
_cod_data_source_block           c4d-2
_cod_database_code               1565518
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C H O'
_shelx_estimated_absorpt_t_max   0.908
_shelx_estimated_absorpt_t_min   0.827
_reflns_odcompleteness_completeness 100.00
_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, All O(H,H) groups
2. Restrained distances
 H6-O2_$1
 2.1 with sigma of 0.02
 H8A-O6_$2
 2 with sigma of 0.02
 H8B-O4_$3
 2 with sigma of 0.02
3.a Free rotating group:
 O8(H8A,H8B)
3.b Ternary CH refined with riding coordinates:
 C11(H11), C12(H12), C13(H13)
3.c Secondary CH2 refined with riding coordinates:
 C16(H16A,H16B), C17(H17A,H17B)
3.d Aromatic/amide H refined with riding coordinates:
 C4(H4A), C5(H5), C8(H8), C15(H15)
3.e Idealised Me refined as rotating group:
 C18(H18A,H18B,H18C)
3.f Idealised tetrahedral OH refined as rotating group:
 O2(H2), O4(H4), O6(H6), O7(H7)
;
_shelx_res_checksum              11372
_shelx_hkl_checksum              48944
_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 1.980
_oxdiff_exptl_absorpt_empirical_full_min 0.434