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_7709350
_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         'C56 H57 N8 Ni2 O6 P, 2(Cl O4), 2(C2 H3 N) '
_chemical_formula_sum            'C60 H63 Cl2 N10 Ni2 O14 P'
_chemical_formula_weight         1367.49
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_date             2020-11-05
_audit_creation_method
;
Olex2 1.3-alpha
(compiled 2020.10.28 svn.r5b043f8a for OlexSys, GUI svn.r6176)
;
_audit_update_record
;
2021-04-23 deposited with the CCDC.	2022-01-24 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 125.491(2)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   46.050(2)
_cell_length_b                   11.3910(5)
_cell_length_c                   28.5228(13)
_cell_measurement_reflns_used    9854
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      30.05
_cell_measurement_theta_min      2.77
_cell_volume                     12182.0(10)
_computing_cell_refinement       'SAINT v8.27A (Bruker, 2012)'
_computing_data_collection       'APEX2 v2012.12-0 (Bruker AXS, 2012)'
_computing_data_reduction        'SAINT v8.27A (Bruker, 2012)'
_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    'SHELXS (Sheldrick, 2008)'
_diffrn_ambient_temperature      100.15
_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 0.998
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device       '\k-geometry diffractometer'
_diffrn_measurement_device_type  'Bruker KAPPA APEX II'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0383
_diffrn_reflns_av_unetI/netI     0.0238
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       55
_diffrn_reflns_limit_h_min       -58
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       36
_diffrn_reflns_limit_l_min       -34
_diffrn_reflns_number            115932
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        26.999
_diffrn_reflns_theta_max         26.999
_diffrn_reflns_theta_min         2.194
_diffrn_source                   'fine focus sealed tube'
_diffrn_source_current           30.0
_diffrn_source_power             1.5
_diffrn_source_type              'Bruker KAPPA APEX Duo'
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.807
_exptl_absorpt_correction_T_max  0.7460
_exptl_absorpt_correction_T_min  0.7056
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2012/1 (Bruker,2012) was used for absorption correction.
wR2(int) was 0.0515 before and 0.0453 after correction.
The Ratio of minimum to maximum transmission is 0.9458.
The \l/2 correction factor is 0.0015.
;
_exptl_crystal_colour            green
_exptl_crystal_colour_primary    green
_exptl_crystal_density_diffrn    1.491
_exptl_crystal_description       column
_exptl_crystal_F_000             5680
_exptl_crystal_size_max          0.298
_exptl_crystal_size_mid          0.219
_exptl_crystal_size_min          0.093
_refine_diff_density_max         0.836
_refine_diff_density_min         -0.476
_refine_diff_density_rms         0.066
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.084
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     905
_refine_ls_number_reflns         13295
_refine_ls_number_restraints     95
_refine_ls_restrained_S_all      1.090
_refine_ls_R_factor_all          0.0511
_refine_ls_R_factor_gt           0.0404
_refine_ls_shift/su_max          0.003
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0326P)^2^+38.5843P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0917
_refine_ls_wR_factor_ref         0.0964
_reflns_Friedel_coverage         0.000
_reflns_number_gt                11285
_reflns_number_total             13295
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1dt03813c2.cif
_cod_data_source_block           g2327
_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_original_cell_volume        12181.9(10)
_cod_database_code               7709350
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.929
_shelx_estimated_absorpt_t_min   0.795
_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. Restrained distances
 C1SB-C2SB
 1.456 with sigma of 0.01
 C1SB-N1SB
 1.137 with sigma of 0.01
 C2SB-N1SB
 2.593 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
N1SB \\sim C1SB \\sim C2SB: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08 within 2A
Uanis(N1S) \\sim Ueq, Uanis(C1S) \\sim Ueq: with sigma of 0.005 and sigma for
terminal atoms of 0.01
Uanis(O24) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(O23) \\sim Ueq, Uanis(O21) \\sim Ueq, Uanis(Cl2) \\sim Ueq, Uanis(O22)
\\sim Ueq, Uanis(O24) \\sim Ueq, Uanis(O23) \\sim Ueq, Uanis(Cl2B) \\sim Ueq,
Uanis(O28) \\sim Ueq, Uanis(Cl2C) \\sim Ueq, Uanis(O25) \\sim Ueq, Uanis(O27)
\\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(N2SB) \\sim Ueq, Uanis(C3SB) \\sim Ueq, Uanis(C4SB) \\sim Ueq: with sigma
of 0.01 and sigma for terminal atoms of 0.02
4. Rigid body (RIGU) restrains
 N1SB, C1SB, C2SB
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Fixed Sof: Cl2(0.8) Cl2B(0.1) Cl2C(0.1) O21(0.8) O22(0.9) O23(0.9) O24(0.9)
 O25(0.1) O26(0.2) O27(0.1) O28(0.1) N2S(0.75) C3S(0.75) C4S(0.75) H4SA(0.75)
 H4SB(0.75) H4SC(0.75) N1S(0.75) C1S(0.75) C2S(0.75) H2SA(0.75) H2SB(0.75)
 H2SC(0.75) N2SB(0.25) C3SB(0.25) C4SB(0.25) H4SD(0.25) H4SE(0.25) H4SF(0.25)
 N1SB(0.25) C1SB(0.25) C2SB(0.25) H2SD(0.25) H2SE(0.25) H2SF(0.25)
6.a Riding coordinates:
 C2S(H2SA,H2SB,H2SC)
6.b Free rotating group:
 N1SB(C1SB,C2SB)
6.c Secondary CH2 refined with riding coordinates:
 C11(H11A,H11B), C12(H12A,H12B), C22(H22A,H22B), C31(H31A,H31B), C32(H32A,
 H32B), C42(H42A,H42B)
6.d Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C9(H9), C10(H10), C14(H14), C15(H15), C16(H16), C24(H24),
 C25(H25), C26(H26), C34(H34), C35(H35), C36(H36), C44(H44), C45(H45), C46(H46),
  C112(H112), C111(H111), C110(H110), C109(H109), C108(H108), C106(H106),
 C105(H105), C104(H104), C103(H103), C102(H102)
6.e Idealised Me refined as rotating group:
 C18(H18A,H18B,H18C), C28(H28A,H28B,H28C), C38(H38A,H38B,H38C), C48(H48A,H48B,
 H48C), C66(H66A,H66B,H66C), C68(H68A,H68B,H68C), C4S(H4SA,H4SB,H4SC),
 C4SB(H4SD,H4SE,H4SF), C2SB(H2SD,H2SE,H2SF)
;
_shelx_res_checksum              98030
_shelx_hkl_checksum              76636
_olex2_submission_special_instructions 'No special instructions were received'