Pyrimidine Nucleosides from <i>Streptomyces</i> sp. SSA28.
Xu, Cheng-Dong; Zhang, Hao-Jian; Ma, Zhong-Jun; Journal of natural products 82 (2019) 2509–2516; doi:10.1021/acs.jnatprod.9b00260

data_1552704
_publ_section_title
;
 Pyrimidine Nucleosides from <i>Streptomyces</i> sp. SSA28.
;
_journal_issue                   9
_journal_name_full               'Journal of natural products'
_journal_page_first              2509
_journal_page_last               2516
_journal_paper_doi               10.1021/acs.jnatprod.9b00260
_journal_volume                  82
_journal_year                    2019
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C10 H15 N3 O3'
_chemical_formula_sum            'C10 H15 N3 O3'
_chemical_formula_weight         225.25
_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'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2019-01-30
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                90
_cell_angle_beta                 98.643(2)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   9.6749(2)
_cell_length_b                   10.4511(2)
_cell_length_c                   10.9170(2)
_cell_measurement_reflns_used    12961
_cell_measurement_temperature    293.68(10)
_cell_measurement_theta_max      73.5010
_cell_measurement_theta_min      4.0530
_cell_volume                     1091.32(4)
_computing_cell_refinement       'CrysAlisPro 1.171.38.43f (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.38.43f (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.38.43f (Rigaku OD, 2015)'
_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 (Sheldrick, 2015)'
_diffrn_ambient_environment      air
_diffrn_ambient_temperature      293.68(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2684
_diffrn_detector_type            AtlasS2
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.977
_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   -129.00  47.00   1.00    1.00    --  -41.11   0.00  30.00  176
  2  \w    -66.00  33.00   1.00    1.00    --  -41.11  38.00-120.00   99
  3  \w     23.00  97.00   1.00    1.00    --   41.11-125.00 -30.00   74
  4  \w      1.00  82.00   1.00    1.00    --   41.11 -99.00 120.00   81
  5  \w     23.00  97.00   1.00    1.00    --   41.11-125.00  60.00   74
  6  \w     81.00 178.00   1.00    1.00    --  106.95  45.00 120.00   97
  7  \w     25.00 160.00   1.00    1.00    --  106.95 -15.00 150.00  135
  8  \w     30.00 115.00   1.00    1.00    --  106.95-110.00 -78.00   85
  9  \w     31.00 135.00   1.00    1.00    --  106.95 -30.00 -90.00  104
 10  \w     34.00 121.00   1.00    1.00    --  106.95-125.00 120.00   87
 11  \w     74.00 178.00   1.00    1.00    --  106.95  77.00 -90.00  104
 12  \w     94.00 178.00   1.00    1.00    --  106.95 125.00 -60.00   84
 13  \w     34.00 121.00   1.00    1.00    --  106.95-125.00 -30.00   87
 14  \w     31.00 140.00   1.00    1.00    --  106.95 -77.00 -60.00  109
 15  \w     81.00 178.00   1.00    1.00    --  106.95  45.00-150.00   97
 16  \w     94.00 178.00   1.00    1.00    --  106.95 125.00 -30.00   84
 17  \w     35.00 136.00   1.00    1.00    --  106.95 -61.00  60.00  101
 18  \w   -113.00 -13.00   1.00    1.00    --  -41.11 -57.00   0.00  100
 19  \w   -117.00  -9.00   1.00    1.00    --  -41.11 -77.00-150.00  108
 20  \w   -117.00  -9.00   1.00    1.00    --  -41.11 -77.00 -90.00  108
 21  \w   -117.00  -9.00   1.00    1.00    --  -41.11 -77.00   0.00  108
 22  \w      9.00 117.00   1.00    1.00    --   41.11  77.00 150.00  108
 23  \w     74.00 178.00   1.00    1.00    --  106.95  77.00  30.00  104
 24  \w     79.00 178.00   1.00    1.00    --  106.95  30.00   0.00   99
 25  \w     78.00 115.00   1.00    1.00    --  106.95  61.00-120.00   37
 26  \w     74.00 178.00   1.00    1.00    --  106.95  77.00 150.00  104
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at zero, AtlasS2'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0817501000
_diffrn_orient_matrix_UB_12      -0.1233426000
_diffrn_orient_matrix_UB_13      0.0402078000
_diffrn_orient_matrix_UB_21      0.1386779000
_diffrn_orient_matrix_UB_22      0.0741936000
_diffrn_orient_matrix_UB_23      0.0075890000
_diffrn_orient_matrix_UB_31      -0.0066028000
_diffrn_orient_matrix_UB_32      0.0321885000
_diffrn_orient_matrix_UB_33      0.1365955000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0350
_diffrn_reflns_av_unetI/netI     0.0256
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.977
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       13
_diffrn_reflns_limit_l_min       -11
_diffrn_reflns_number            16623
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.966
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.846
_diffrn_reflns_theta_min         4.096
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.858
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.69772
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.38.43f (Rigaku Oxford Diffraction, 2015)
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    1.371
_exptl_crystal_description       block
_exptl_crystal_F_000             480
_exptl_crystal_size_max          0.12
_exptl_crystal_size_mid          0.11
_exptl_crystal_size_min          0.09
_refine_diff_density_max         0.211
_refine_diff_density_min         -0.181
_refine_diff_density_rms         0.040
_refine_ls_abs_structure_details
;
 Flack x determined using 1917 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.05(6)
_refine_ls_extinction_coef       0.0069(5)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.084
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     310
_refine_ls_number_reflns         4328
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.084
_refine_ls_R_factor_all          0.0285
_refine_ls_R_factor_gt           0.0278
_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^)+(0.0355P)^2^+0.2561P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0718
_refine_ls_wR_factor_ref         0.0756
_reflns_Friedel_coverage         0.871
_reflns_Friedel_fraction_full    0.996
_reflns_Friedel_fraction_max     0.954
_reflns_number_gt                4252
_reflns_number_total             4328
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            np9b00260_si_003.cif
_cod_data_source_block           muhe
_cod_database_code               1552704
_shelx_shelxl_version_number     2018/3
_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
2.a Ternary CH refined with riding coordinates:
 C5B(H5B), C8(H8), C9(H9), C9B(H9B), C5(H5), C8B(H8B)
2.b Secondary CH2 refined with riding coordinates:
 C6(H6A,H6B), C7(H7A,H7B), C6B(H6BA,H6BB), C7B(H7BA,H7BB)
2.c Aromatic/amide H refined with riding coordinates:
 C4(H4), C3(H3A), C3B(H3BA), C2B(H2B)
2.d Idealised Me refined as rotating group:
 C10(H10D,H10E,H10F), C10B(H10A,H10B,H10C)
2.e Idealised tetrahedral OH refined as rotating group:
 O3(H3), O3B(H3B)
;
_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 1.211
_oxdiff_exptl_absorpt_empirical_full_min 0.637