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_4346550
_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_sum            'C46 H39 B Cl2 F4 Fe Ni O2 P2 S2'
_chemical_formula_weight         1022.10
_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   geom
_audit_creation_date             2015-07-16
_audit_creation_method
; 
Olex2 1.2 
(compiled 2015.01.26 svn.r3150 for OlexSys, GUI svn.r4998) 
;
_cell_angle_alpha                90
_cell_angle_beta                 97.862(12)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   35.637(9)
_cell_length_b                   11.475(3)
_cell_length_c                   22.627(5)
_cell_measurement_reflns_used    9671
_cell_measurement_temperature    296(2)
_cell_measurement_theta_max      26.195
_cell_measurement_theta_min      2.479
_cell_volume                     9166(4)
_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    'SHELX-2013-4 (Sheldrick, 2013)'
_diffrn_ambient_temperature      296.15
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.996
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_radiation_wavelength_id  cd82s_0m
_diffrn_reflns_av_R_equivalents  0.0323
_diffrn_reflns_av_unetI/netI     0.0130
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.996
_diffrn_reflns_limit_h_max       44
_diffrn_reflns_limit_h_min       -44
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       28
_diffrn_reflns_limit_l_min       -28
_diffrn_reflns_number            142161
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.996
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         26.465
_diffrn_reflns_theta_min         2.110
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    1.059
_exptl_absorpt_correction_T_max  0.8224
_exptl_absorpt_correction_T_min  0.5051
_exptl_absorpt_correction_type   integration
_exptl_absorpt_process_details
; 
SADABS-2014/5 (Bruker,2014/5) was used for absorption correction. 
wR2(int) was 0.0854 before and 0.0455 after correction. 
The Ratio of minimum to maximum transmission is 0.6142. 
The \l/2 correction factor is Not present. 
;
_exptl_crystal_colour            red
_exptl_crystal_density_diffrn    1.481
_exptl_crystal_description       prism
_exptl_crystal_F_000             4176
_exptl_crystal_id                CpNiFeSPh0
_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 -1 2 scattering 
planes roughly normal to the spindle axis. 
;
_exptl_crystal_size_max          0.491
_exptl_crystal_size_mid          0.187
_exptl_crystal_size_min          0.134
_refine_diff_density_max         0.994
_refine_diff_density_min         -0.902
_refine_diff_density_rms         0.082
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.060
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     668
_refine_ls_number_reflns         9432
_refine_ls_number_restraints     783
_refine_ls_restrained_S_all      1.107
_refine_ls_R_factor_all          0.0671
_refine_ls_R_factor_gt           0.0557
_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^)+(0.0881P)^2^+31.6576P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1606
_refine_ls_wR_factor_ref         0.1740
_reflns_Friedel_coverage         0.000
_reflns_number_gt                7886
_reflns_number_total             9432
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ic5b01662_si_002.cif
_cod_data_source_block           cm29ubsa_a
_cod_database_code               4346550
_shelxl_version_number           2014-3
_shelx_estimated_absorpt_t_max   0.871
_shelx_estimated_absorpt_t_min   0.624
_olex2_refinement_description
; 
1. Fixed Uiso 
 At 1.2 times of: 
  All C(H) groups, All C(H,H) groups 
2. Restrained distances 
 P2-C40 \\sim P2-C40A 
 with sigma of 0.02 
 P1-C20A \\sim P1-C20 
 with sigma of 0.02 
 P2-C34A \\sim P2-C34 
 with sigma of 0.02 
 S2-C12A \\sim S2-C12 
 with sigma of 0.02 
 B1-F1 \\sim B1-F2 \\sim B1-F3 \\sim B1-F4 \\sim B1A-F1A \\sim B1A-F2A \\sim 
B1A-F3A \\sim B1A-F4A 
 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 0.02 
 C46-Cl1 \\sim C46-Cl2 \\sim C46A-Cl1A \\sim C46A-Cl2A 
 with sigma of 0.01 
 Cl1-Cl2 \\sim Cl1A-Cl2A 
 with sigma of 0.02 
3. Uiso/Uaniso restraints and constraints 
C40 \\sim C41 \\sim C42 \\sim C43 \\sim C44 \\sim C45 \\sim C40A \\sim C41A 
\\sim C42A \\sim C43A \\sim C44A \\sim C45A: within 1.7A with sigma of 0.04 and 
sigma for terminal atoms of 0.08 
C20 \\sim C21 \\sim C22 \\sim C23 \\sim C24 \\sim C25 \\sim C21A \\sim C20A 
\\sim C22A \\sim C23A \\sim C24A \\sim C25A: within 1.7A with sigma of 0.04 and 
sigma for terminal atoms of 0.08 
C34 \\sim C39 \\sim C38 \\sim C37 \\sim C36 \\sim C35 \\sim C34A \\sim C39A 
\\sim C38A \\sim C37A \\sim C36A \\sim C35A: within 1.7A with sigma of 0.04 and 
sigma for terminal atoms of 0.08 
C16 \\sim C15 \\sim C14 \\sim C13 \\sim C12 \\sim C17 \\sim C12A \\sim C17A 
\\sim C16A \\sim C15A \\sim C14A \\sim C13A: within 1.7A with sigma of 0.04 and 
sigma for terminal atoms of 0.08 
B1 \\sim F1 \\sim F2 \\sim F3 \\sim F4 \\sim B1A \\sim F1A \\sim F2A \\sim F3A 
\\sim F4A: within 1.7A with sigma of 0.04 and sigma for terminal atoms of 0.08 
Cl1 \\sim Cl2 \\sim C46 \\sim Cl1A \\sim Cl2A \\sim C46A: within 1.7A with 
sigma of 0.04 and sigma for terminal atoms of 0.08 
4. Others 
 Sof(C40A)=Sof(C41A)=Sof(H41A)=Sof(C42A)=Sof(H42A)=Sof(C43A)=Sof(H43A)= 
 Sof(C44A)=Sof(H44A)=Sof(C45A)=Sof(H45A)=1-FVAR(1) 
 Sof(C40)=Sof(C41)=Sof(H41)=Sof(C42)=Sof(H42)=Sof(C43)=Sof(H43)=Sof(C44)= 
 Sof(H44)=Sof(C45)=Sof(H45)=FVAR(1) 
 Sof(C20A)=Sof(C21A)=Sof(H21A)=Sof(C22A)=Sof(H22A)=Sof(C23A)=Sof(H23A)= 
 Sof(C24A)=Sof(H24A)=Sof(C25A)=Sof(H25A)=1-FVAR(2) 
 Sof(C20)=Sof(C21)=Sof(H21)=Sof(C22)=Sof(H22)=Sof(C23)=Sof(H23)=Sof(C24)= 
 Sof(H24)=Sof(C25)=Sof(H25)=FVAR(2) 
 Sof(C34A)=Sof(C35A)=Sof(H35A)=Sof(C36A)=Sof(H36A)=Sof(C37A)=Sof(H37A)= 
 Sof(C38A)=Sof(H38A)=Sof(C39A)=Sof(H39A)=1-FVAR(3) 
 Sof(C34)=Sof(C35)=Sof(H35)=Sof(C36)=Sof(H36)=Sof(C37)=Sof(H37)=Sof(C38)= 
 Sof(H38)=Sof(C39)=Sof(H39)=FVAR(3) 
 Sof(C12A)=Sof(C13A)=Sof(H13A)=Sof(C14A)=Sof(H14A)=Sof(C15A)=Sof(H15A)= 
 Sof(C16A)=Sof(H16A)=Sof(C17A)=Sof(H17A)=1-FVAR(4) 
 Sof(C12)=Sof(C13)=Sof(H13)=Sof(C14)=Sof(H14)=Sof(C15)=Sof(H15)=Sof(C16)= 
 Sof(H16)=Sof(C17)=Sof(H17)=FVAR(4) 
 Sof(B1A)=Sof(F1A)=Sof(F2A)=Sof(F3A)=Sof(F4A)=1-FVAR(5) 
 Sof(B1)=Sof(F1)=Sof(F2)=Sof(F3)=Sof(F4)=FVAR(5) 
 Sof(Cl1A)=Sof(Cl2A)=Sof(C46A)=Sof(H46C)=Sof(H46D)=1-FVAR(6) 
 Sof(Cl1)=Sof(Cl2)=Sof(C46)=Sof(H46A)=Sof(H46B)=FVAR(6) 
5.a Secondary CH2 refined with riding coordinates: 
 C46(H46A,H46B), C46A(H46C,H46D) 
5.b Aromatic/amide H refined with riding coordinates: 
 C1(H1), C2(H2), C3(H3), C4(H4), C5(H5), C7(H7), C8(H8), C9(H9), C10(H10), 
 C11(H11), C13(H13), C14(H14), C15(H15), C16(H16), C17(H17), C13A(H13A), 
 C14A(H14A), C15A(H15A), C16A(H16A), C17A(H17A), C21(H21), C22(H22), C23(H23), 
C24(H24), C25(H25), C21A(H21A), C22A(H22A), C23A(H23A), C24A(H24A), C25A(H25A),
 C27(H27), C28(H28), C29(H29), C30(H30), C31(H31), C32(H32), C33(H33), 
 C35(H35), C36(H36), C37(H37), C38(H38), C39(H39), C35A(H35A), C36A(H36A), 
 C37A(H37A), C38A(H38A), C39A(H39A), C41(H41), C42(H42), C43(H43), C44(H44), 
 C45(H45), C41A(H41A), C42A(H42A), C43A(H43A), C44A(H44A), C45A(H45A) 
5.c Fitted hexagon refined as free rotating group: 
 C12(C13,C14,C15,C16,C17), C12A(C13A,C14A,C15A,C16A,C17A), C20(C21,C22,C23,C24, 
C25), C20A(C21A,C22A,C23A,C24A,C25A), C34(C35,C36,C37,C38,C39), C34A(C35A,C36A,
 C37A,C38A,C39A), C40(C41,C42,C43,C44,C45), C40A(C41A,C42A,C43A,C44A,C45A) 
;
_olex2_submission_special_instructions 'No special instructions were received'