Cyanide Docking and Linkage Isomerism in Models for the Artificial [FeFe]-Hydrogenase Maturation Process.
Sil, Debangsu; Martinez, Zachary; Ding, Shengda; Bhuvanesh, Nattamai; Darensbourg, Donald J.; Hall, Michael B.; Darensbourg, Marcetta Y.; Journal of the American Chemical Society 140 (2018) 9904–9911; doi:10.1021/jacs.8b04189

data_4132476
_publ_section_title
;
 Cyanide Docking and Linkage Isomerism in Models for the Artificial
 [FeFe]-Hydrogenase Maturation Process.
;
_journal_issue                   31
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              9904
_journal_page_last               9911
_journal_paper_doi               10.1021/jacs.8b04189
_journal_volume                  140
_journal_year                    2018
_chemical_formula_moiety
'2(C27 H24 Cu Fe2 N5 O5 S2), F6 P, 2(C2 H3 N1)'
_chemical_formula_sum            'C58 H54 Cu2 F6 Fe4 N12 O10 P S4'
_chemical_formula_weight         1702.82
_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'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2017-10-24
_audit_creation_method
;
Olex2 1.2-beta
(compiled 2017.03.28 svn.r3405 for OlexSys, GUI svn.r5335)
;
_cell_angle_alpha                90
_cell_angle_beta                 91.307(2)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   19.4349(7)
_cell_length_b                   11.9765(4)
_cell_length_c                   14.9472(5)
_cell_measurement_reflns_used    9830
_cell_measurement_temperature    100
_cell_measurement_theta_max      69.977
_cell_measurement_theta_min      4.337
_cell_volume                     3478.2(2)
_computing_cell_refinement       'SAINT v8.37A (Bruker, 2015)'
_computing_data_reduction        'SAINT v8.37A (Bruker, 2015)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL (Sheldrick, 2008)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100.0
_diffrn_measured_fraction_theta_full 0.994
_diffrn_measured_fraction_theta_max 0.993
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0585
_diffrn_reflns_av_unetI/netI     0.0361
_diffrn_reflns_Laue_measured_fraction_full 0.994
_diffrn_reflns_Laue_measured_fraction_max 0.993
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       18
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            38157
_diffrn_reflns_point_group_measured_fraction_full 0.994
_diffrn_reflns_point_group_measured_fraction_max 0.993
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         70.056
_diffrn_reflns_theta_min         2.274
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    9.203
_exptl_absorpt_correction_T_max  0.3841
_exptl_absorpt_correction_T_min  0.2331
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'SADABS-2016/2 (Bruker,2016/2) was used for absorption correction. wR2(int) was 0.0950 before and 0.0681 after correction. The Ratio of minimum to maximum transmission is 0.6069. The \l/2 correction factor is Not present.'
_exptl_crystal_colour            brown
_exptl_crystal_colour_primary    brown
_exptl_crystal_density_diffrn    1.626
_exptl_crystal_description       block
_exptl_crystal_F_000             1722
_exptl_crystal_size_max          0.226
_exptl_crystal_size_mid          0.118
_exptl_crystal_size_min          0.073
_refine_diff_density_max         0.938
_refine_diff_density_min         -0.541
_refine_diff_density_rms         0.102
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.086
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     485
_refine_ls_number_reflns         6568
_refine_ls_number_restraints     224
_refine_ls_restrained_S_all      1.081
_refine_ls_R_factor_all          0.0687
_refine_ls_R_factor_gt           0.0584
_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^)+(0.0572P)^2^+13.8959P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1460
_refine_ls_wR_factor_ref         0.1526
_reflns_Friedel_coverage         0.000
_reflns_number_gt                5557
_reflns_number_total             6568
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja8b04189_si_003.cif
_cod_data_source_block           pdtcn_cua
_cod_database_code               4132476
_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, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C3S-C2S = C3T-C2T
 1.48 with sigma of 0.01
 N5T-C3T
 2.575 with sigma of 0.005
 C2-C1 \\sim C2A-C1 \\sim C3-C2 \\sim C3-C2A
 with sigma of 0.01
 Fe1-C7A \\sim Fe1-C7
 with sigma of 0.005
 O5-C7 \\sim O5A-C7A
 with sigma of 0.005
 C3S-C2S \\sim C3T-C2T
 with sigma of 0.005
 N5S-C2S \\sim N5T-C2T
 with sigma of 0.005
3. Uiso/Uaniso restraints and constraints
N5S \\sim C2S \\sim C3S: within 2A with sigma of 0.02 and sigma for terminal
atoms of 0.01
S2 \\sim C2 \\sim C3 \\sim C2A \\sim C1 \\sim S1: within 2A with sigma of 0.02
and sigma for terminal atoms of 0.02
Fe1 \\sim C7A \\sim C7 \\sim O5A \\sim O5: within 2A with sigma of 0.005 and
sigma for terminal atoms of 0.01
C3T \\sim N5T \\sim C2T \\sim C3S \\sim N5S \\sim C2S: within 2A with sigma of
0.005 and sigma for terminal atoms of 0.01
Uanis(C2) = Uanis(C2A)
Uanis(N5T) = Uanis(N5S)
4. Rigid body (RIGU) restrains
 N5S, C2S, C3S
 with sigma for 1-2 distances of 0.02 and sigma for 1-3 distances of 0.005
 C3, C2, C2A, C1, S2
 with sigma for 1-2 distances of 0.02 and sigma for 1-3 distances of 0.01
 Fe1, C7A, C7, O5A, O5
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 N5S, C2S, C3S, C3T, N5T, C2T
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
5. Same fragment restrains
{N5S, C2S, C3S} sigma for 1-2: 0.005, 1-3: 0.04
as
{N5T, C2T, C3T}
6. Others
 Sof(H1BC)=Sof(H1BD)=Sof(H3BC)=Sof(H3BD)=Sof(C2A)=Sof(H2AA)=Sof(H2AB)=Sof(C7A)=
 Sof(O5A)=1-FVAR(1)
 Sof(O5)=Sof(H1AA)=Sof(H1AB)=Sof(C2)=Sof(H2A)=Sof(H2B)=Sof(H3AA)=Sof(H3AB)=
 Sof(C7)=FVAR(1)
 Sof(N5T)=Sof(C2T)=Sof(C3T)=Sof(H3TA)=Sof(H3TB)=Sof(H3TC)=1-FVAR(2)
 Sof(N5S)=Sof(C2S)=Sof(C3S)=Sof(H3SA)=Sof(H3SB)=Sof(H3SC)=FVAR(2)
7.a Secondary CH2 refined with riding coordinates:
 C1(H1AA,H1AB), C1(H1BC,H1BD), C2(H2A,H2B), C3(H3AA,H3AB), C3(H3BC,H3BD),
 C15(H15A,H15B), C21(H21A,H21B), C27(H27A,H27B), C2A(H2AA,H2AB)
7.b Aromatic/amide H refined with riding coordinates:
 C10(H10), C11(H11), C12(H12), C13(H13), C16(H16), C17(H17), C18(H18),
 C19(H19), C22(H22), C23(H23), C24(H24), C25(H25)
7.c Idealised Me refined as rotating group:
 C3S(H3SA,H3SB,H3SC), C3T(H3TA,H3TB,H3TC)
;
_shelx_res_checksum              32660
_shelx_hkl_checksum              19768
_olex2_submission_special_instructions 'No special instructions were received'