Cytidine Deaminase Can Deaminate Fused Pyrimidine Ribonucleosides
Ludford III, Paul T; Li, Yao; Yang, Shenghua; Tor, Yitzhak; Organic & Biomolecular Chemistry  (2021) –; doi:10.1039/D1OB00705J

data_7158078
_publ_section_title
;
 Cytidine Deaminase Can Deaminate Fused Pyrimidine Ribonucleosides
;
_journal_name_full               'Organic &amp; Biomolecular Chemistry'
_journal_paper_doi               10.1039/D1OB00705J
_journal_year                    2021
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C33 H26 N2 O9 S'
_chemical_formula_sum            'C33 H26 N2 O9 S'
_chemical_formula_weight         626.62
_space_group_crystal_system      triclinic
_space_group_IT_number           1
_space_group_name_Hall           'P 1'
_space_group_name_H-M_alt        'P 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2019-04-30
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2021-04-05 deposited with the CCDC.	2021-05-05 downloaded from the CCDC.
;
_cell_angle_alpha                71.1950(10)
_cell_angle_beta                 85.3720(10)
_cell_angle_gamma                85.7510(10)
_cell_formula_units_Z            2
_cell_length_a                   5.40480(10)
_cell_length_b                   13.6367(4)
_cell_length_c                   20.6903(6)
_cell_measurement_reflns_used    9515
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      72.53
_cell_measurement_theta_min      3.43
_cell_volume                     1436.97(7)
_computing_cell_refinement       'SAINT V8.38A (?, 2016)'
_computing_data_reduction        'SAINT V8.38A (?, 2016)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL (Sheldrick, 2008)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100.15
_diffrn_detector                 'Bruker APEX2 area detector'
_diffrn_detector_area_resol_mean 7.9
_diffrn_detector_type            'CCD area detector'
_diffrn_measured_fraction_theta_full 0.983
_diffrn_measured_fraction_theta_max 0.965
_diffrn_measurement_device       'three-circle diffractometer'
_diffrn_measurement_device_type  'Bruker SMART APEX2 area detector'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_monochromator  'mirror optics'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0329
_diffrn_reflns_av_unetI/netI     0.0465
_diffrn_reflns_Laue_measured_fraction_full 0.983
_diffrn_reflns_Laue_measured_fraction_max 0.965
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       16
_diffrn_reflns_limit_k_min       -16
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            23073
_diffrn_reflns_point_group_measured_fraction_full 0.932
_diffrn_reflns_point_group_measured_fraction_max 0.894
_diffrn_reflns_theta_full        67.500
_diffrn_reflns_theta_max         72.648
_diffrn_reflns_theta_min         2.260
_diffrn_source                   'microfocus sealed X-ray tube'
_diffrn_source_type              'Incoatec I\ms'
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    1.536
_exptl_absorpt_correction_T_max  0.7536
_exptl_absorpt_correction_T_min  0.6731
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'SADABS-2016/2 (Bruker,2016/2) was used for absorption correction. wR2(int) was 0.0738 before and 0.0614 after correction. The Ratio of minimum to maximum transmission is 0.8932. The \l/2 correction factor is Not present.'
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.448
_exptl_crystal_description       block
_exptl_crystal_F_000             652
_exptl_crystal_size_max          0.22
_exptl_crystal_size_mid          0.08
_exptl_crystal_size_min          0.06
_refine_diff_density_max         0.207
_refine_diff_density_min         -0.197
_refine_diff_density_rms         0.038
_refine_ls_abs_structure_details
;
 Flack x determined using 4365 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.024(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.027
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     813
_refine_ls_number_reflns         10240
_refine_ls_number_restraints     3
_refine_ls_restrained_S_all      1.026
_refine_ls_R_factor_all          0.0285
_refine_ls_R_factor_gt           0.0273
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0376P)^2^+0.0182P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0695
_refine_ls_wR_factor_ref         0.0701
_reflns_Friedel_coverage         0.853
_reflns_Friedel_fraction_full    0.880
_reflns_Friedel_fraction_max     0.823
_reflns_number_gt                9898
_reflns_number_total             10240
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1ob00705j2.cif
_cod_data_source_block           tor_mthu3
_cod_database_code               7158078
_shelx_shelxl_version_number     2014/7
_shelx_estimated_absorpt_t_max   0.913
_shelx_estimated_absorpt_t_min   0.729
_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
2.a Ternary CH refined with riding coordinates:
 C8(H8), C9(H9), C10(H10), C11(H11), C8'(H8'), C9'(H9'), C10'(H10'), C11'(H11')
2.b Secondary CH2 refined with riding coordinates:
 C12(H12A,H12B), C12'(H12C,H12D)
2.c Aromatic/amide H refined with riding coordinates:
 N1(H1), C7(H7), C15(H15), C16(H16), C17(H17), C18(H18), C19(H19), C22(H22),
 C23(H23), C24(H24), C25(H25), C26(H26), C29(H29), C30(H30), C31(H31), C32(H32),
  C33(H33), N1'(H1'), C7'(H7'), C15'(H15'), C16'(H16'), C17'(H17'), C18'(H18'),
 C19'(H19'), C22'(H22'), C23'(H23'), C24'(H24'), C25'(H25'), C26'(H26'),
 C29'(H29'), C30'(H30'), C31'(H31'), C32'(H32'), C33'(H33')
2.d Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C1'(H1'A,H1'B,H1'C)
;
_shelx_res_checksum              34469
_olex2_submission_special_instructions 'No special instructions were received'