Oxygen Uptake in Complexes Related to [NiFeS] and [NiFeSe] Hydrogenase Active Sites
Yang, Xuemei; Elrod, Lindy C.; Reibenspies, Joseph; Hall, Michael B.; Darensbourg, Marcetta Y.; Chemical Science  (2019) –; doi:10.1039/C8SC04436H

data_1550185
_publ_section_title
;
 Oxygen Uptake in Complexes Related to [NiFeS] and [NiFeSe] Hydrogenase
 Active Sites
;
_journal_name_full               'Chemical Science'
_journal_paper_doi               10.1039/C8SC04436H
_journal_year                    2019
_chemical_formula_moiety
'C8.69 H14.25 N1.18 Ni0.59 S1.18, 0.41(C14 H22 N2 Ni1 S2)'
_chemical_formula_sum            'C14.4 H23.21 N2 Ni S2'
_chemical_formula_weight         347.25
_chemical_name_systematic        NiSPh
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_symmetry_space_group_name_Hall  '-P 2ybc'
_symmetry_space_group_name_H-M   'P 1 21/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_audit_creation_date             2018-04-26
_audit_creation_method
;
Olex2 1.2
(compiled 2017.08.10 svn.r3458 for OlexSys, GUI svn.r5381)
;
_audit_update_record
;
2018-08-11 deposited with the CCDC.
2018-11-05 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 93.156(3)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   9.6130(7)
_cell_length_b                   10.3609(7)
_cell_length_c                   15.3479(10)
_cell_measurement_reflns_used    9979
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      72.51
_cell_measurement_theta_min      4.27
_cell_volume                     1526.32(18)
_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  'XH (Sheldrick, 2008)'
_computing_structure_solution    'SIR2004 (Burla et al., 2007)'
_diffrn_ambient_temperature      100.0
_diffrn_detector                 'CCD area detector'
_diffrn_detector_area_resol_mean 7.9
_diffrn_detector_type            'Bruker SMART CCD APEX2 area detector'
_diffrn_measured_fraction_theta_full 0.995
_diffrn_measured_fraction_theta_max 0.994
_diffrn_measurement_device       'three-circle diffractometer'
_diffrn_measurement_device_type  'Bruker SMART CCD APEX2 area detector'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0395
_diffrn_reflns_av_unetI/netI     0.0202
_diffrn_reflns_Laue_measured_fraction_full 0.995
_diffrn_reflns_Laue_measured_fraction_max 0.994
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            28502
_diffrn_reflns_point_group_measured_fraction_full 0.995
_diffrn_reflns_point_group_measured_fraction_max 0.994
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         72.504
_diffrn_reflns_theta_min         5.153
_diffrn_source                   'sealed X-ray tube'
_diffrn_source_target            Mo
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    4.286
_exptl_absorpt_correction_T_max  0.7536
_exptl_absorpt_correction_T_min  0.4486
_exptl_absorpt_correction_type   none
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1139 before and 0.0651 after correction.
The Ratio of minimum to maximum transmission is 0.5953.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            'dark purple'
_exptl_crystal_density_diffrn    1.511
_exptl_crystal_F_000             735
_refine_diff_density_max         0.382
_refine_diff_density_min         -0.931
_refine_diff_density_rms         0.086
_refine_ls_extinction_coef       0.0024(3)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2017/1 (Sheldrick 2017)'
_refine_ls_goodness_of_fit_ref   1.065
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     347
_refine_ls_number_reflns         3013
_refine_ls_number_restraints     417
_refine_ls_restrained_S_all      1.055
_refine_ls_R_factor_all          0.0629
_refine_ls_R_factor_gt           0.0603
_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^)+(0.0088P)^2^+9.0000P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1330
_refine_ls_wR_factor_ref         0.1343
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2856
_reflns_number_total             3013
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c8sc04436h2.cif
_cod_data_source_block           myd
_cod_original_formula_sum        'C14.40 H23.21 N2 Ni S2'
_cod_database_code               1550185
_shelx_shelxl_version_number     2017/1
_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 planarity
 C9_1, C10_1, C11_1, C12_1, C13_1, C14_1
 C9_2, C10_2, C11_2, C12_2, C13_2, C14_2
 with sigma of 0.1
3. Rigid bond restraints
 Ni1_1, S1_1, S2_1, N1_1, N2_1, C1_1, C2_1, C3_1, C4_1, C5_1, C6_1, C7_1, C8_1,
  C9_1, C10_1, C11_1, C12_1, C13_1, C14_1
 Ni1_2, S1_2, S2_2, N1_2, N2_2, C1_2, C2_2, C3_2, C4_2, C5_2, C6_2, C7_2, C8_2,
  C9_2, C10_2, C11_2, C12_2, C13_2, C14_2
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
4. Uiso/Uaniso restraints and constraints
Ni1_1 \\sim S1_1 \\sim S2_1 \\sim N1_1 \\sim N2_1 \\sim C1_1 \\sim C2_1 \\sim
C3_1 \\sim C4_1 \\sim C5_1 \\sim C6_1 \\sim C7_1 \\sim C8_1 \\sim C9_1 \\sim
C10_1 \\sim C11_1 \\sim C12_1 \\sim C13_1 \\sim C14_1 \\sim Ni1_2 \\sim S1_2
\\sim S2_2 \\sim N1_2 \\sim N2_2 \\sim C1_2 \\sim C2_2 \\sim C3_2 \\sim C4_2
\\sim C5_2 \\sim C6_2 \\sim C7_2 \\sim C8_2 \\sim C9_2 \\sim C10_2 \\sim C11_2
\\sim C12_2 \\sim C13_2 \\sim C14_2: within 2A with sigma of 0.004 and sigma
for terminal atoms of 0.01
5. Same fragment restrains
{Ni1_2, S1_2, S2_2, N1_2, N2_2, C1_2, C2_2, C3_2, C4_2, C5_2, C6_2, C7_2, C8_2,
C9_2, C10_2, C11_2, C12_2, C13_2, C14_2}
as
{Ni1_1, S1_1, S2_1, N1_1, N2_1, C1_1, C2_1, C3_1, C4_1, C5_1, C6_1, C7_1, C8_1,
C9_1, C10_1, C11_1, C12_1, C13_1, C14_1} sigma for 1-2: 0.005 1-3: 0.04
6. Others
 Sof(Ni1)=Sof(S1)=Sof(S2)=Sof(N1)=Sof(N2)=Sof(C1)=Sof(H1A)=Sof(H1B)=Sof(C2)=
 Sof(H2A)=Sof(H2B)=Sof(C3)=Sof(H3A)=Sof(H3B)=Sof(C4)=Sof(H4A)=Sof(H4B)=Sof(C5)=
 Sof(H5A)=Sof(H5B)=Sof(C6)=Sof(H6A)=Sof(H6B)=Sof(C7)=Sof(H7A)=Sof(H7B)=Sof(C8)=
 Sof(H8A)=Sof(H8B)=Sof(H8C)=Sof(C9)=Sof(C10)=Sof(H10)=Sof(C11)=Sof(H11)=
 Sof(C12)=Sof(H12)=Sof(C13)=Sof(H13)=Sof(C14)=Sof(H14)=1-FVAR(1)
 Sof(Ni1)=Sof(S1)=Sof(S2)=Sof(N1)=Sof(N2)=Sof(C1)=Sof(H1A)=Sof(H1B)=Sof(C2)=
 Sof(H2A)=Sof(H2B)=Sof(C3)=Sof(H3A)=Sof(H3B)=Sof(C4)=Sof(H4A)=Sof(H4B)=Sof(C5)=
 Sof(H5A)=Sof(H5B)=Sof(C6)=Sof(H6A)=Sof(H6B)=Sof(C7)=Sof(H7A)=Sof(H7B)=Sof(C9)=
 Sof(C10)=Sof(H10)=Sof(C11)=Sof(H11)=Sof(C12)=Sof(H12)=Sof(C13)=Sof(H13)=
 Sof(C14)=Sof(H14)=FVAR(1)
7.a Secondary CH2 refined with riding coordinates:
 C1(H1A,H1B), C2(H2A,H2B), C3(H3A,H3B), C4(H4A,H4B), C5(H5A,H5B), C6(H6A,H6B),
 C7(H7A,H7B), C1(H1A,H1B), C2(H2A,H2B), C3(H3A,H3B), C4(H4A,H4B), C5(H5A,H5B),
 C6(H6A,H6B), C7(H7A,H7B)
7.b Aromatic/amide H refined with riding coordinates:
 C10(H10), C11(H11), C12(H12), C13(H13), C14(H14), C10(H10), C11(H11),
 C12(H12), C13(H13), C14(H14)
7.c Idealised Me refined as rotating group:
 C8(H8A,H8B,H8C), C8(H8A,H8B,H8C)
;
_olex2_submission_special_instructions 'No special instructions were received'