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_1552703
_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         'C15 H23 N3 O5'
_chemical_formula_sum            'C15 H23 N3 O5'
_chemical_formula_weight         325.36
_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             2019-01-29
_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                   9.06338(13)
_cell_length_b                   10.86547(13)
_cell_length_c                   17.5252(2)
_cell_measurement_reflns_used    9024
_cell_measurement_temperature    293.68(10)
_cell_measurement_theta_max      73.2670
_cell_measurement_theta_min      2.4740
_cell_volume                     1725.84(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 0.993
_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   -121.00   0.00   1.00    1.00    --  -40.98 -19.00 150.00  121
  2  \w     23.00  97.00   1.00    1.00    --   40.98-125.00  30.00   74
  3  \w    -33.00  66.00   1.00    1.00    --   40.98 -38.00-180.00   99
  4  \w     79.00 178.00   1.00    2.29    --  106.95  30.00 -90.00   99
  5  \w     34.00 121.00   1.00    2.29    --  106.95-125.00 150.00   87
  6  \w     81.00 178.00   1.00    2.29    --  106.95  45.00 -60.00   97
  7  \w     35.00 136.00   1.00    2.29    --  106.95 -61.00 -30.00  101
  8  \w     25.00 109.00   1.00    2.29    --  106.95 -95.00 -30.00   84
  9  \w   -117.00  -8.00   1.00    1.00    --  -40.98 -77.00 -30.00  109
 10  \w   -115.00 -16.00   1.00    1.00    --  -40.98 -38.00  60.00   99
 11  \w     54.00 178.00   1.00    4.00    --  106.95  15.00  90.00  124
 12  \w     35.00 136.00   1.00    4.00    --  106.95 -61.00 150.00  101
 13  \w     81.00 178.00   1.00    4.00    --  106.95  45.00   0.00   97
 14  \w     79.00 129.00   1.00    4.00    --  106.95  30.00-180.00   50
;
_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      -0.0097197000
_diffrn_orient_matrix_UB_12      -0.0697813000
_diffrn_orient_matrix_UB_13      0.0764070000
_diffrn_orient_matrix_UB_21      -0.0021098000
_diffrn_orient_matrix_UB_22      -0.1233403000
_diffrn_orient_matrix_UB_23      -0.0433863000
_diffrn_orient_matrix_UB_31      0.1695529000
_diffrn_orient_matrix_UB_32      -0.0054593000
_diffrn_orient_matrix_UB_33      0.0039472000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0291
_diffrn_reflns_av_unetI/netI     0.0221
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.993
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       21
_diffrn_reflns_limit_l_min       -21
_diffrn_reflns_number            13705
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.985
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.536
_diffrn_reflns_theta_min         4.789
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.789
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.83693
_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    1.252
_exptl_crystal_description       block
_exptl_crystal_F_000             696
_exptl_crystal_size_max          0.12
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.08
_refine_diff_density_max         0.593
_refine_diff_density_min         -0.217
_refine_diff_density_rms         0.056
_refine_ls_abs_structure_details
;
 Flack x determined using 1366 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.02(7)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.180
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     216
_refine_ls_number_reflns         3437
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.181
_refine_ls_R_factor_all          0.0427
_refine_ls_R_factor_gt           0.0413
_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^)+(0.0380P)^2^+1.1220P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1049
_refine_ls_wR_factor_ref         0.1057
_reflns_Friedel_coverage         0.725
_reflns_Friedel_fraction_full    0.999
_reflns_Friedel_fraction_max     0.973
_reflns_number_gt                3352
_reflns_number_total             3437
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            np9b00260_si_002.cif
_cod_data_source_block           16d
_cod_database_code               1552703
_shelx_shelxl_version_number     2017/1
_shelx_estimated_absorpt_t_max   0.940
_shelx_estimated_absorpt_t_min   0.911
_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, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Restrained distances
 O5-H5
 0.82 with sigma of 0.02
3.a Ternary CH refined with riding coordinates:
 C5(H5A), C2(H2), C1(H1A)
3.b Secondary CH2 refined with riding coordinates:
 C4(H4A,H4B), C3(H3A,H3B), C11(H11A,H11B)
3.c Aromatic/amide H refined with riding coordinates:
 N3(H3), C7(H7), C6(H6)
3.d Idealised Me refined as rotating group:
 C00L(H00A,H00B,H00C), C13(H13A,H13B,H13C), C14(H14A,H14B,H14C)
3.e Idealised tetrahedral OH refined as rotating group:
 O1(H1)
;
_shelx_res_checksum              99573
_shelx_hkl_checksum              7545
_shelx_fab_checksum              38819
_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 1.420
_oxdiff_exptl_absorpt_empirical_full_min 0.667