Terminal {Ni(II)-SH} complex promoted anaerobic catalytic sulfur atom transfer reaction: implication to the sulfide oxidase function of Cu/Zn-superoxide dismutase.
Bag, Jayanta; Das, Surajit; Pal, Kuntal; Dalton transactions (Cambridge, England : 2003) 53 (2024) 12773–12782; doi:10.1039/d4dt01364f

data_7716562
_publ_section_title
;
 Terminal {Ni(II)-SH} complex promoted anaerobic catalytic sulfur atom
 transfer reaction: implication to the sulfide oxidase function of
 Cu/Zn-superoxide dismutase.
;
_journal_issue                   30
_journal_name_full
'Dalton transactions (Cambridge, England : 2003)'
_journal_page_first              12773
_journal_page_last               12782
_journal_paper_doi               10.1039/d4dt01364f
_journal_volume                  53
_journal_year                    2024
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C39 H40 N Ni O P S'
_chemical_formula_sum            'C39 H40 N Ni O P S'
_chemical_formula_weight         660.46
_chemical_name_systematic        'ND-249_auto__ final clear data'
_space_group_crystal_system      orthorhombic
_space_group_IT_number           29
_space_group_name_Hall           'P 2c -2ac'
_space_group_name_H-M_alt        'P c a 21'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_block_doi                 10.5517/ccdc.csd.cc2j6h6g
_audit_creation_date             2024-01-31
_audit_creation_method
;
Olex2 1.3-alpha
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6408)
;
_audit_update_record
;
2024-01-31 deposited with the CCDC.	2024-07-04 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   19.25730(10)
_cell_length_b                   13.21440(10)
_cell_length_c                   13.09390(10)
_cell_measurement_reflns_used    39802
_cell_measurement_temperature    101(1)
_cell_measurement_theta_max      68.0200
_cell_measurement_theta_min      3.3160
_cell_volume                     3332.05(4)
_computing_cell_refinement       'CrysAlisPro 1.171.42.73a (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.42.73a (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.42.73a (Rigaku OD, 2022)'
_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  'XL  (Sheldrick, 2008)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      101(1)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix3000
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.999
_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    -43.00  26.00   0.50    0.25    --  -40.58  38.00-150.00  138
  2  \w    -57.00  26.00   0.50    0.25    --  -40.58  50.00  60.00  166
  3  \w    -31.00  30.00   0.50    0.25    --  -40.58  25.00-150.00  122
  4  \w    -24.00  35.00   0.50    0.25    --  -40.58  12.00 150.00  118
  5  \w    -31.00  30.00   0.50    0.25    --  -40.58  25.00  90.00  122
  6  \w   -113.00 -17.00   0.50    0.25    --  -40.58 -18.00-160.34  192
  7  \w    -24.00  35.00   0.50    0.25    --  -40.58  12.00   0.00  118
  8  \w    -78.00   4.00   0.50    0.25    --  -40.58 104.00-120.00  164
  9  \w   -107.00 -25.00   0.50    0.25    --  -40.58 -38.00  60.00  164
 10  \w     41.00 100.00   0.50    0.25    --   40.58-138.00-180.00  118
 11  \w      4.00 116.00   0.50    0.25    --   40.58  12.00-150.00  224
 12  \w      8.00  42.00   0.50    0.25    --   40.58  92.00 109.42   68
 13  \w     18.00  78.00   0.50    0.25    --   40.58-104.00   0.00  120
 14  \w     41.00 100.00   0.50    0.25    --   40.58-138.00  30.00  118
 15  \w    -29.00  31.00   0.50    0.25    --   40.58 -25.00-120.00  120
 16  \w     12.00  43.00   0.50    0.25    --   40.58  83.00 -20.37   62
 17  \w     13.00  43.00   0.50    0.25    --   40.58  81.00-170.89   60
 18  \w      8.00  42.00   0.50    0.25    --   40.58  92.00  -2.84   68
 19  \w    -47.00 -15.00   0.50    1.45    --  -82.50  42.00  90.00   64
 20  \w    -47.00 -15.00   0.50    1.45    --  -82.50  42.00 -60.00   64
 21  \w    -47.00 -15.00   0.50    1.45    --  -82.50  42.00   0.00   64
 22  \w    -47.00 -15.00   0.50    1.45    --  -82.50  42.00  60.00   64
 23  \w    -47.00 -15.00   0.50    1.45    --  -82.50  42.00 -90.00   64
 24  \w   -101.00 -23.00   0.50    1.45    --  -82.50 145.00  30.00  156
 25  \w    -47.00 -15.00   0.50    1.45    --  -82.50  42.00  30.00   64
 26  \w    -57.00 -16.00   0.50    1.45    --  -82.50  50.00 -30.00   82
 27  \w   -146.00 -78.00   0.50    1.45    --  -82.50-117.00 -60.00  136
 28  \w     44.00 127.00   0.50    1.45    --   96.35-145.00  60.00  166
 29  \w     33.00 110.00   0.50    1.45    --   96.35-117.00 -60.00  154
 30  \w     99.00 160.00   0.50    1.45    --   96.35 117.00 -90.00  122
 31  \w    105.00 170.00   0.50    1.45    --   96.35  96.00 -60.00  130
 32  \w     29.00  83.00   0.50    1.45    --   96.35 -68.00 -90.00  108
 33  \w     44.00 127.00   0.50    1.45    --   96.35-145.00 -90.00  166
 34  \w     30.00  57.00   0.50    1.45    --   96.35 -50.00 150.00   54
 35  \w     71.00 170.00   0.50    1.45    --   96.35  17.00 120.00  198
 36  \w     80.00 164.00   0.50    1.45    --   96.35  42.00  60.00  168
 37  \w     70.00 165.00   0.50    1.45    --   96.35  77.00-150.00  190
 38  \w     28.00  68.00   0.50    1.45    --   96.35 -59.00   0.00   80
 39  \w     26.00 127.00   0.50    1.45    --   96.35 -87.00-120.00  202
 40  \w     28.00  68.00   0.50    1.45    --   96.35 -59.00 -60.00   80
 41  \w     44.00 127.00   0.50    1.45    --   96.35-145.00-120.00  166
 42  \w     80.00 164.00   0.50    1.45    --   96.35  42.00 -30.00  168
 43  \w     29.00  83.00   0.50    1.45    --   96.35 -68.00-120.00  108
 44  \w     26.00 127.00   0.50    1.45    --   96.35 -87.00  60.00  202
 45  \w     33.00 110.00   0.50    1.45    --   96.35-117.00  60.00  154
 46  \w     29.00  83.00   0.50    1.45    --   96.35 -68.00  90.00  108
 47  \w     33.00 110.00   0.50    1.45    --   96.35-117.00 -90.00  154
 48  \w     70.00 165.00   0.50    1.45    --   96.35  77.00 -30.00  190
 49  \w     29.00  83.00   0.50    1.45    --   96.35 -68.00  60.00  108
 50  \w     30.00  57.00   0.50    1.45    --   96.35 -50.00  90.00   54
 51  \w     28.00 105.00   0.50    1.45    --   96.35 -77.00 150.00  154
 52  \w     33.00 110.00   0.50    1.45    --   96.35-117.00  90.00  154
 53  \w     72.00 164.00   0.50    1.45    --   96.35  68.00 -90.00  184
 54  \w     72.00 164.00   0.50    1.45    --   96.35  68.00-120.00  184
 55  \w     99.00 160.00   0.50    1.45    --   96.35 117.00 -30.00  122
 56  \w     83.00 164.00   0.50    1.45    --   96.35  33.00  30.00  162
 57  \w   -108.00 -17.00   0.50    0.25    --  -40.58 -64.00 -60.00  182
 58  \w   -107.00 -21.00   0.50    0.25    --  -40.58 -50.00  30.00  172
 59  \w   -108.00 -17.00   0.50    0.25    --  -40.58 -64.00  90.00  182
 60  \w   -109.00 -14.00   0.50    0.25    --  -40.58 -77.00-150.00  190
 61  \w   -107.00 -21.00   0.50    0.25    --  -40.58 -50.00 150.00  172
 62  \w   -108.00 -17.00   0.50    0.25    --  -40.58 -64.00   0.00  182
 63  \w     18.00 108.00   0.50    0.25    --   40.58  64.00 -60.00  180
 64  \w      8.00  42.00   0.50    0.25    --   40.58  92.00  94.05   68
 65  \w     12.00  43.00   0.50    0.25    --   40.58  83.00 -44.34   62
 66  \w     18.00 108.00   0.50    0.25    --   40.58  64.00  30.00  180
 67  \w     13.00  43.00   0.50    0.25    --   40.58  81.00 176.93   60
 68  \w      8.00  42.00   0.50    0.25    --   40.58  92.00-103.87   68
 69  \w     13.00  43.00   0.50    0.25    --   40.58  81.00 142.71   60
 70  \w      8.00  35.00   0.50    0.25    --   40.58  93.00 -61.98   54
 71  \w     10.00  43.00   0.50    0.25    --   40.58  87.00-151.16   66
 72  \w     13.00  43.00   0.50    0.25    --   40.58  80.00 -96.61   60
 73  \w     72.00 148.00   0.50    1.45    --   96.35  68.00 120.00  152
 74  \w     83.00 164.00   0.50    1.45    --   96.35  33.00-180.00  162
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix3000'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0725593000
_diffrn_orient_matrix_UB_12      0.0479118000
_diffrn_orient_matrix_UB_13      -0.0109731000
_diffrn_orient_matrix_UB_21      -0.0247726000
_diffrn_orient_matrix_UB_22      -0.0932500000
_diffrn_orient_matrix_UB_23      -0.0605269000
_diffrn_orient_matrix_UB_31      -0.0228368000
_diffrn_orient_matrix_UB_32      -0.0510074000
_diffrn_orient_matrix_UB_33      0.1002830000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0684
_diffrn_reflns_av_unetI/netI     0.0304
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       15
_diffrn_reflns_limit_k_min       -15
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            54454
_diffrn_reflns_point_group_measured_fraction_full 0.974
_diffrn_reflns_point_group_measured_fraction_max 0.971
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.136
_diffrn_reflns_theta_min         3.345
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.115
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.72718
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.73a (Rigaku Oxford Diffraction, 2022)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear dark red'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   dark
_exptl_crystal_colour_primary    red
_exptl_crystal_density_diffrn    1.317
_exptl_crystal_description       block
_exptl_crystal_F_000             1392
_exptl_crystal_preparation       'slow diffusion CH2Cl2 with Et2O'
_exptl_crystal_recrystallization_method '100 k'
_exptl_crystal_size_max          0.21
_exptl_crystal_size_mid          0.14
_exptl_crystal_size_min          0.12
_refine_diff_density_max         0.213
_refine_diff_density_min         -0.308
_refine_diff_density_rms         0.037
_refine_ls_abs_structure_details
;
 Flack x determined using 2595 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.035(18)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.079
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     403
_refine_ls_number_reflns         5907
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.079
_refine_ls_R_factor_all          0.0344
_refine_ls_R_factor_gt           0.0338
_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^)+(0.0646P)^2^+0.6936P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0924
_refine_ls_wR_factor_ref         0.0933
_reflns_Friedel_coverage         0.855
_reflns_Friedel_fraction_full    0.946
_reflns_Friedel_fraction_max     0.941
_reflns_number_gt                5803
_reflns_number_total             5907
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4dt01364f2.cif
_cod_data_source_block           2tBu
_cod_depositor_comments
'Adding full bibliography for 7716561--7716564.cif.'
_cod_database_code               7716562
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         'C H O Ni P S'
_chemical_oxdiff_usercomment     100K
_shelx_estimated_absorpt_t_max   0.785
_shelx_estimated_absorpt_t_min   0.665
_reflns_odcompleteness_completeness 100.00
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_olex2_refinement_description
;
1.a Aromatic/amide H refined with riding coordinates:
 C1(H1), C5(H5), C7(H7), C9(H9), C10(H10), C11(H11), C12(H12), C23(H23),
 C24(H24), C25(H25), C26(H26), C27(H27), C29(H29), C30(H30), C31(H31), C32(H32),
  C33(H33), C35(H35), C36(H36), C37(H37), C38(H38), C39(H39)
1.b Idealised Me refined as rotating group:
 C15(H15A,H15B,H15C), C16(H16A,H16B,H16C), C17(H17A,H17B,H17C), C19(H19A,H19B,
 H19C), C20(H20A,H20B,H20C), C21(H21A,H21B,H21C)
;
_shelx_res_checksum              96222
_olex2_exptl_crystal_mounting_method loop
_olex2_submission_original_sample_id 'ND-249_auto__ final clear data'
_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 1.344
_oxdiff_exptl_absorpt_empirical_full_min 0.685