Crystal structure of a nucleoside model for the interstrand cross-link formed by the reaction of 2'-deoxyguanosine and an abasic site in duplex DNA
Catalano, Michael J.; Ruddraraju, Kasi Viswanatharaju; Barnes, Charles L.; Gates, Kent S.; Acta Crystallographica Section E 72 (2016) 624–627; doi:10.1107/S205698901600517X

data_2241633
_publ_section_title
;
 Crystal structure of a nucleoside model for the interstrand cross-link
 formed by the reaction of 2'-deoxyguanosine and an abasic site in duplex
 DNA
;
_journal_coeditor_code           HB7568
_journal_issue                   5
_journal_name_full               'Acta Crystallographica Section E'
_journal_page_first              624
_journal_page_last               627
_journal_paper_doi               10.1107/S205698901600517X
_journal_volume                  72
_journal_year                    2016
_chemical_formula_iupac          'C17 H25 N5 O7'
_chemical_formula_moiety         'C17 H25 N5 O7'
_chemical_formula_sum            'C17 H25 N5 O7'
_chemical_formula_weight         411.42
_chemical_name_systematic
9-[(2<i>R</i>,4<i>S</i>,5<i>R</i>)-4-Hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-2-{[(2<i>R</i>,4<i>S</i>,5<i>R</i>)-4-methoxy-5-(methoxymethyl)tetrahydrofuran-2-yl]amino}-1<i>H</i>-purin-6(9<i>H</i>)-one
_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'
_symmetry_cell_setting           monoclinic
_symmetry_space_group_name_Hall  'P 2yb'
_symmetry_space_group_name_H-M   'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_method           SHELXL-2014/7
_cell_angle_alpha                90
_cell_angle_beta                 98.0230(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   8.18170(10)
_cell_length_b                   26.4033(5)
_cell_length_c                   8.8800(2)
_cell_measurement_reflns_used    9940
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      72.2
_cell_measurement_theta_min      5.3
_cell_volume                     1899.52(6)
_computing_cell_refinement
;
SAINT (Bruker, 2008)
;
_computing_data_collection
;
APEX2 (Bruker, 2008)
;
_computing_data_reduction
;
SAINT (Bruker, 2008)
;
_computing_molecular_graphics
;
X-SEED, Barbour, 2001
;
_computing_publication_material
;
<i>CIFTAB</i> (Sheldrick, 2008)
;
_computing_structure_refinement
;
SHELXL2013 (Sheldrick, 2015)
;
_computing_structure_solution
;
SHELXS2013 (Sheldrick, 2008)
;
_diffrn_ambient_temperature      100(2)
_diffrn_measured_fraction_theta_full 0.988
_diffrn_measured_fraction_theta_max 0.984
_diffrn_measurement_device_type  'Bruker APEXII CCD'
_diffrn_measurement_method       'omega and phi scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0292
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       31
_diffrn_reflns_limit_k_min       -31
_diffrn_reflns_limit_l_max       10
_diffrn_reflns_limit_l_min       -9
_diffrn_reflns_number            26696
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         72.154
_diffrn_reflns_theta_min         3.348
_diffrn_standards_decay_%        0.0
_exptl_absorpt_coefficient_mu    0.956
_exptl_absorpt_correction_T_max  0.93
_exptl_absorpt_correction_T_min  0.86
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
(SADABS; Sheldrick, 2008)
;
_exptl_crystal_colour            Colourless
_exptl_crystal_density_diffrn    1.439
_exptl_crystal_description       Prism
_exptl_crystal_F_000             872
_exptl_crystal_size_max          0.150
_exptl_crystal_size_mid          0.080
_exptl_crystal_size_min          0.080
_refine_diff_density_max         0.225
_refine_diff_density_min         -0.167
_refine_ls_abs_structure_details
;
Flack <i>x</i> determined using 2923 quotients
[(<i>I</i>^+^)-(<i>I</i>^-^)]/[(<i>I</i>^+^)+(<i>I</i>^-^)]
(Parsons et al., 2013)
;
_refine_ls_abs_structure_Flack   0.08(5)
_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     531
_refine_ls_number_reflns         6862
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.038
_refine_ls_R_factor_all          0.0284
_refine_ls_R_factor_gt           0.0270
_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^)+(0.0424P)^2^+0.3476P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0704
_refine_ls_wR_factor_ref         0.0715
_reflns_number_gt                6644
_reflns_number_total             6862
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            hb7568sup1.cif
_cod_data_source_block           I
_cod_original_sg_symbol_H-M      'P 21'
_cod_database_code               2241633
_cod_database_fobs_code          2241633
_shelx_estimated_absorpt_t_min   0.870
_shelx_estimated_absorpt_t_max   0.927
_shelx_hkl_checksum              93723
_shelx_res_checksum              83100