Models of the Ni-L and Ni-SIa States of the [NiFe]-Hydrogenase Active Site.
Chambers, Geoffrey M.; Huynh, Mioy T.; Li, Yulong; Hammes-Schiffer, Sharon; Rauchfuss, Thomas B.; Reijerse, Edward; Lubitz, Wolfgang; Inorganic chemistry 55 (2016) 419–431; doi:10.1021/acs.inorgchem.5b01662

data_4346549
_publ_section_title
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 Models of the Ni-L and Ni-SIa States of the [NiFe]-Hydrogenase Active
 Site.
;
_journal_issue                   2
_journal_name_full               'Inorganic chemistry'
_journal_page_first              419
_journal_page_last               431
_journal_paper_doi               10.1021/acs.inorgchem.5b01662
_journal_volume                  55
_journal_year                    2016
_chemical_formula_moiety         'C37 H39 Fe Ni O P2 S2, B F4'
_chemical_formula_sum            'C37 H39 B F4 Fe Ni O P2 S2'
_chemical_formula_weight         827.11
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_audit_creation_date             2014-09-18
_audit_creation_method
; 
Olex2 1.2 
(compiled 2014.07.22 svn.r2960 for OlexSys, GUI svn.r4862) 
;
_cell_angle_alpha                90
_cell_angle_beta                 106.2980(19)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   10.4724(18)
_cell_length_b                   30.158(5)
_cell_length_c                   12.995(2)
_cell_measurement_reflns_used    9914
_cell_measurement_temperature    179(2)
_cell_measurement_theta_max      26.05
_cell_measurement_theta_min      2.22
_cell_volume                     3939.2(11)
_computing_cell_refinement       'SAINT V8.34A (Bruker, 2005)'
_computing_data_collection       'APEX2 V2013.10-0 (Bruker, 2013)'
_computing_data_reduction
; 
SAINT V8.34A, XPREP v2013/3, SADABS V2012/1, TWINABS V2012/1 
(Bruker, 2012 & 2013) 
;
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELX-2013-4 (Sheldrick, 2013)'
_computing_structure_solution    Olex2
_diffrn_ambient_temperature      179.15
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.999
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_radiation_wavelength_id  fm22a_0m
_diffrn_reflns_av_R_equivalents  0.0978
_diffrn_reflns_av_unetI/netI     0.0586
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       12
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       37
_diffrn_reflns_limit_k_min       -37
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            45343
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         26.151
_diffrn_reflns_theta_min         1.350
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    1.080
_exptl_absorpt_correction_T_max  0.7453
_exptl_absorpt_correction_T_min  0.6437
_exptl_absorpt_correction_type   integration
_exptl_absorpt_process_details
; 
SADABS-2008/1 (Bruker,2008) was used for absorption correction. 
wR2(int) was 0.0865 before and 0.0512 after correction. 
The Ratio of minimum to maximum transmission is 0.8637. 
The \l/2 correction factor is 0.0015. 
;
_exptl_crystal_colour            'dark red'
_exptl_crystal_colour_modifier   dark
_exptl_crystal_colour_primary    red
_exptl_crystal_density_diffrn    1.395
_exptl_crystal_description       prism
_exptl_crystal_F_000             1704
_exptl_crystal_id                CpNiFeMe2pdt
_exptl_crystal_preparation
; 
The data crystal was mounted using oil (Parantone-N, Exxon) to a 
0.3 mm cryo-loop (Hampton Research) with the 1 -3 0 face scattering 
planes roughly normal to the spindle axis. 
;
_exptl_crystal_size_max          0.51
_exptl_crystal_size_mid          0.276
_exptl_crystal_size_min          0.118
_refine_diff_density_max         0.357
_refine_diff_density_min         -0.388
_refine_diff_density_rms         0.057
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   0.942
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     543
_refine_ls_number_reflns         7860
_refine_ls_number_restraints     653
_refine_ls_restrained_S_all      0.954
_refine_ls_R_factor_all          0.0485
_refine_ls_R_factor_gt           0.0339
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0449P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0846
_refine_ls_wR_factor_ref         0.0885
_reflns_Friedel_coverage         0.000
_reflns_number_gt                5938
_reflns_number_total             7860
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ic5b01662_si_002.cif
_cod_data_source_block           fm22a2_0m
_cod_original_cell_volume        3939.3(12)
_cod_database_code               4346549
_shelxl_version_number           2014-3
_shelx_estimated_absorpt_t_max   0.883
_shelx_estimated_absorpt_t_min   0.609
_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 
 F4-B1 \\sim F4A-B1 \\sim F1-B1 \\sim F1A-B1 \\sim F2A-B1 \\sim F2-B1 \\sim 
F3A-B1 \\sim F3-B1 
 with sigma of 0.01 
 F1-F2 \\sim F1-F3 \\sim F1-F4 \\sim F2-F3 \\sim F2-F4 \\sim F3-F4 \\sim 
F1A-F2A \\sim F1A-F3A \\sim F1A-F4A ~ 
 F2A-F3A \\sim F2A-F4A \\sim F3A-F4A 
 with sigma of 0.01 
 P2-C15 \\sim P2-C19A 
 with sigma of 0.02 
 P1-C26A \\sim P1-C26 
 with sigma of 0.02 
3. Uiso/Uaniso restraints and constraints 
F1A \\sim F1 \\sim F3 \\sim F3A \\sim F2A \\sim F2 \\sim F2A \\sim F2 \\sim F4 
\\sim F4A: within 1.7A with sigma of 0.01 and sigma for terminal atoms of 0.02 
C29 \\sim C26 \\sim C26A \\sim C27 \\sim C31 \\sim C27A \\sim C31A \\sim C28 
\\sim H27 \\sim H31 \\sim C30 \\sim C28A \\sim H27A \\sim C30A \\sim H31A \\sim 
H28 \\sim H30 \\sim C29A \\sim H28A \\sim H30A \\sim H29 \\sim H29A: within 
1.7A with sigma of 0.01 and sigma for terminal atoms of 0.02 
C15A \\sim C15 \\sim C19A \\sim C14 \\sim C19 \\sim C14A \\sim C17 \\sim C16 
\\sim C17A \\sim C18A \\sim C18 \\sim C16A: within 1.7A with sigma of 0.01 and 
sigma for terminal atoms of 0.02 
Uanis(F2) \\sim Ueq, Uanis(F1) \\sim Ueq, Uanis(F4) \\sim Ueq, Uanis(F3) \\sim 
Ueq, Uanis(F2A) \\sim Ueq, Uanis(F1A) \\sim Ueq, Uanis(F4A) \\sim Ueq, 
Uanis(F3A) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02 
4. Others 
 Sof(F2A)=Sof(F1A)=Sof(F4A)=Sof(F3A)=1-FVAR(1) 
 Sof(F2)=Sof(F1)=Sof(F4)=Sof(F3)=FVAR(1) 
 Sof(C30A)=Sof(H30A)=Sof(C29A)=Sof(H29A)=Sof(C28A)=Sof(H28A)=Sof(C27A)= 
 Sof(H27A)=Sof(C26A)=Sof(C31A)=Sof(H31A)=1-FVAR(2) 
 Sof(C28)=Sof(H28)=Sof(C27)=Sof(H27)=Sof(C26)=Sof(C31)=Sof(H31)=Sof(C30)= 
 Sof(H30)=Sof(C29)=Sof(H29)=FVAR(2) 
 Sof(C17A)=Sof(H17A)=Sof(C14A)=Sof(H14A)=Sof(C19A)=Sof(C15A)=Sof(H15A)= 
 Sof(C18A)=Sof(H18A)=Sof(C16A)=Sof(H16A)=1-FVAR(3) 
 Sof(C17)=Sof(H17)=Sof(C14)=Sof(H14)=Sof(C15)=Sof(C19)=Sof(H19)=Sof(C16)= 
 Sof(H16)=Sof(C18)=Sof(H18)=FVAR(3) 
5.a Secondary CH2 refined with riding coordinates: 
 C6(H6A,H6B), C13(H13A,H13B), C8(H8A,H8B), C12(H12A,H12B) 
5.b Aromatic/amide H refined with riding coordinates: 
C37(H37), C34(H34), C4(H4), C36(H36), C1(H1), C2(H2), C5(H5), C24(H24), 
C33(H33), C25(H25), C21(H21), C3(H3), C23(H23), C22(H22), C17(H17), C14(H14), 
C19(H19), C16(H16), C18(H18), C35(H35), C28(H28), C27(H27), C31(H31), C30(H30), 
C29(H29), C30A(H30A), C29A(H29A), C28A(H28A), C27A(H27A), C31A(H31A), 
C17A(H17A), C14A(H14A), C15A(H15A), C18A(H18A), C16A(H16A) 
5.c Fitted hexagon refined as free rotating group: 
 C17(C14,C15,C19,C16,C18), C28(C27,C26,C31,C30,C29), C30A(C29A,C28A,C27A,C26A, 
 C31A), C17A(C14A,C19A,C15A,C18A,C16A) 
5.d Idealised Me refined as rotating group: 
 C10(H10A,H10B,H10C), C9(H9A,H9B,H9C) 
;
_smtbx_masks_special_details
; 
Two voids were masked from the unit cell. Both voids possessed identcal 
volumes of 179.7 A^3 and contained residual electron density equivalent 
to 40.3 electrons each. The molecules present in the voids were predicted 
to be tetrahydrofuran, which is predicted to contain 40 electrons. 
;
_olex2_submission_special_instructions 'No special instructions were received'