Evaluation of the Binding Mode of a Cytotoxic Dinuclear Nickel Complex to two Neighboring Phosphates of the DNA Backbone
Simon, Jasmin; Horstmann, Claudia; Mix, Andreas; Stammler, Anja; Oldengott, Jan; Bögge, Hartmut; Glaser, Thorsten; Dalton Transactions  (2022) –; doi:10.1039/D1DT03813C

data_7709349
_publ_section_title
;
 Evaluation of the Binding Mode of a Cytotoxic Dinuclear Nickel Complex to
 two Neighboring Phosphates of the DNA Backbone
;
_journal_name_full               'Dalton Transactions'
_journal_paper_doi               10.1039/D1DT03813C
_journal_year                    2022
_chemical_formula_moiety         'C64 H65 N6 Ni2 O12 P2, C24 H20 B'
_chemical_formula_sum            'C88 H85 B N6 Ni2 O12 P2'
_chemical_formula_weight         1608.79
_space_group_crystal_system      monoclinic
_space_group_IT_number           13
_space_group_name_Hall           '-P 2yc'
_space_group_name_H-M_alt        'P 1 2/c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_atom_sites_solution_secondary   difmap
_audit_creation_date             2020-10-09
_audit_creation_method
;
Olex2 1.3-alpha
(compiled 2020.09.11 svn.r3730fd0d for OlexSys, GUI svn.r6159)
;
_audit_update_record
;
2021-04-23 deposited with the CCDC.	2022-01-24 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 114.7046(12)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   18.9153(6)
_cell_length_b                   13.8331(4)
_cell_length_c                   16.2657(5)
_cell_measurement_reflns_used    9998
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      68.194
_cell_measurement_theta_min      3.195
_cell_volume                     3866.5(2)
_computing_cell_refinement       'SAINT V8.40A (Bruker, 2019)'
_computing_data_collection       'APEX3 v2016.5-0 (Bruker AXS, 2016)'
_computing_data_reduction        'SAINT V8.40A (Bruker, 2019)'
_computing_molecular_graphics    'Olex2 1.3-alpha (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3-alpha (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/1 (Sheldrick, 2015)'
_diffrn_ambient_temperature      100(2)
_diffrn_detector                 'CCD area detector'
_diffrn_detector_area_resol_mean 7.9
_diffrn_detector_type            'Bruker APEX II area detector'
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device       '\k-geometry diffractometer'
_diffrn_measurement_device_type  'Bruker Kappa APEX Duo'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_monochromator  'QuazarTM Montel Multilayer optics'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0337
_diffrn_reflns_av_unetI/netI     0.0223
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       22
_diffrn_reflns_limit_h_min       -22
_diffrn_reflns_limit_k_max       16
_diffrn_reflns_limit_k_min       -16
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            44608
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         68.301
_diffrn_reflns_theta_min         2.571
_diffrn_source                   'I\mS Incoatec Microfocus Source'
_diffrn_source_current           1.0
_diffrn_source_power             0.04969
_diffrn_source_type              'Bruker KAPPA APEX Duo'
_diffrn_source_voltage           49.69
_diffrn_standards_decay_%        0
_diffrn_standards_interval_count 0
_diffrn_standards_interval_time  0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    1.550
_exptl_absorpt_correction_T_max  0.7531
_exptl_absorpt_correction_T_min  0.6420
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.0667 before and 0.0503 after correction.
The Ratio of minimum to maximum transmission is 0.8525.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            grey
_exptl_crystal_density_diffrn    1.382
_exptl_crystal_description       block
_exptl_crystal_F_000             1684
_exptl_crystal_size_max          0.20
_exptl_crystal_size_mid          0.20
_exptl_crystal_size_min          0.16
_refine_diff_density_max         0.279
_refine_diff_density_min         -0.362
_refine_diff_density_rms         0.041
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.051
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     514
_refine_ls_number_reflns         7090
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.051
_refine_ls_R_factor_all          0.0298
_refine_ls_R_factor_gt           0.0271
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0316P)^2^+1.9547P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0704
_refine_ls_wR_factor_ref         0.0720
_reflns_Friedel_coverage         0.000
_reflns_number_gt                6497
_reflns_number_total             7090
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1dt03813c2.cif
_cod_data_source_block           g2716
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_diffrn_radiation_probe' value 'X-ray' was changed to
'x-ray' in accordance with the
/home/data/users/saulius/crontab/automatic-downloads/rss-feeds/RSC/lib/dictionaries/cif_core.dic
dictionary named 'cif_core.dic' version 2.4.2 last updated on
2011-04-26.

Automatic conversion script
Id: cif_fix_values 7556 2019-12-06 15:28:31Z antanas 
;
_cod_database_code               7709349
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.788
_shelx_estimated_absorpt_t_min   0.746
_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
2.a Secondary CH2 refined with riding coordinates:
 C11(H11A,H11B), C12(H12A,H12B), C22(H22A,H22B)
2.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C14(H14), C15(H15), C16(H16), C24(H24), C25(H25), C26(H26),
 C102(H102), C103(H103), C104(H104), C105(H105), C106(H106), C108(H108),
 C109(H109), C110(H110), C111(H111), C112(H112), C202(H202), C203(H203),
 C204(H204), C205(H205), C206(H206), C208(H208), C209(H209), C210(H210),
 C211(H211), C212(H212)
2.c Idealised Me refined as rotating group:
 C18(H18A,H18B,H18C), C28(H28A,H28B,H28C)
;
_shelx_res_checksum              71295
_shelx_hkl_checksum              74708
_olex2_submission_special_instructions 'No special instructions were received'