Chromophore-Supported Structural and Functional Model of Dinuclear Copper Enzymes, for Facilitating Mechanism of Action Studies
Chen, Qiu-Cheng; Fridman, Natalia; Tumanskii, Boris L.; Gross, Zeev; Chemical Science  (2021) –; doi:10.1039/D1SC02593G

data_1564339
_publ_section_title
;
 Chromophore-Supported Structural and Functional Model of Dinuclear Copper
 Enzymes, for Facilitating Mechanism of Action Studies
;
_journal_name_full               'Chemical Science'
_journal_paper_doi               10.1039/D1SC02593G
_journal_year                    2021
_chemical_formula_moiety         'C57 H21 F20 N5 Pd, 3(C4 H8 O)'
_chemical_formula_sum            'C69 H45 F20 N5 O3 Pd'
_chemical_formula_weight         1478.50
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   geom
_audit_block_doi                 10.5517/ccdc.csd.cc24wl7w
_audit_creation_date             2020-02-16
_audit_creation_method
;
Olex2 1.3
(compiled 2019.11.21 svn.r41b79517 for OlexSys, GUI svn.r6003)
;
_audit_update_record
;
2020-03-25 deposited with the CCDC.	2021-08-09 downloaded from the CCDC.
;
_cell_angle_alpha                89.120(2)
_cell_angle_beta                 86.471(2)
_cell_angle_gamma                86.785(2)
_cell_formula_units_Z            2
_cell_length_a                   7.8433(2)
_cell_length_b                   18.5899(5)
_cell_length_c                   21.0630(5)
_cell_measurement_reflns_used    17859
_cell_measurement_temperature    100.01(10)
_cell_measurement_theta_max      79.0950
_cell_measurement_theta_min      4.7640
_cell_volume                     3060.25(13)
_computing_cell_refinement       'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_computing_molecular_graphics    'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2014/7 (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.01(10)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.997
_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    -37.00  89.00   0.50   11.28    --    0.00  82.00 -90.00  252
  2  \w    -89.00  56.00   0.50   11.28    --    0.00 -19.00 -60.00  290
  3  \w    -35.00  89.00   0.50   11.28    --    0.00  77.00 150.00  248
  4  \w    -35.00  89.00   0.50   11.28    --    0.00  77.00 150.00  248
  5  \w     18.00 145.00   0.50   45.13    --  107.20 -82.00 -30.00  254
  6  \w     18.00 145.00   0.50   45.13    --  107.20 -82.00-180.00  254
  7  \w     18.00 143.00   0.50   45.13    --  107.20 -77.00 150.00  250
  8  \w     18.00 197.00   0.50   45.13    --  107.20  15.00 120.00  358
  9  \w     18.00 145.00   0.50   45.13    --  107.20 -82.00  90.00  254
 10  \w     18.00 145.00   0.50   45.13    --  107.20 -82.00-150.00  254
 11  \w     77.00 197.00   0.50   45.13    --  107.20  45.00-120.00  240
 12  \w     18.00 145.00   0.50   45.13    --  107.20 -82.00 -90.00  254
 13  \w     70.00 197.00   0.50   45.13    --  107.20  82.00 120.00  254
 14  \w     18.00 145.00   0.50   45.13    --  107.20 -82.00  30.00  254
 15  \w     77.00 197.00   0.50   45.13    --  107.20  61.00 -30.00  240
 16  \w     18.00 138.00   0.50   45.13    --  107.20 -61.00  30.00  240
 17  \w     77.00 179.00   0.50   45.13    --  107.20  45.00 -90.00  204
 18  \w     20.00 111.00   0.50   45.13    --  107.20 -30.00 -60.00  182
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC12 (RINC): Kappa dual home/near'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.1599148000
_diffrn_orient_matrix_UB_12      -0.0008929000
_diffrn_orient_matrix_UB_13      -0.0463327000
_diffrn_orient_matrix_UB_21      -0.0374765000
_diffrn_orient_matrix_UB_22      0.0803880000
_diffrn_orient_matrix_UB_23      -0.0154646000
_diffrn_orient_matrix_UB_31      0.1089397000
_diffrn_orient_matrix_UB_32      0.0206682000
_diffrn_orient_matrix_UB_33      0.0546332000
_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  0.0591
_diffrn_reflns_av_unetI/netI     0.0434
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       22
_diffrn_reflns_limit_k_min       -22
_diffrn_reflns_limit_l_max       25
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            47309
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.997
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         70.067
_diffrn_reflns_theta_min         4.206
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    3.475
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.863
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.46 (Rigaku Oxford Diffraction, 2018)
Numerical absorption correction based on gaussian integration over
			a multifaceted crystal model
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.605
_exptl_crystal_description       needle
_exptl_crystal_F_000             1488
_exptl_crystal_size_max          0.075
_exptl_crystal_size_mid          0.029
_exptl_crystal_size_min          0.023
_refine_diff_density_max         1.428
_refine_diff_density_min         -1.110
_refine_diff_density_rms         0.092
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.131
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     929
_refine_ls_number_reflns         11605
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.131
_refine_ls_R_factor_all          0.0759
_refine_ls_R_factor_gt           0.0706
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0858P)^2^+6.0371P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1806
_refine_ls_wR_factor_ref         0.1841
_reflns_Friedel_coverage         0.000
_reflns_number_gt                10505
_reflns_number_total             11605
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1sc02593g2.cif
_cod_data_source_block           zg11
_cod_database_code               1564339
_shelx_shelxl_version_number     2014/7
_chemical_oxdiff_formula         C55H18F20N5Pd1
_chemical_oxdiff_usercomment     'vial 2 perfluorinated ether'
_reflns_odcompleteness_completeness 99.69
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     69.95
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
2. Others
 Sof(Pd1A)=Sof(H1)=Sof(C49A)=Sof(H49C)=Sof(H49D)=Sof(C50A)=Sof(H50A)=Sof(C51A)=
 Sof(H51A)=Sof(C52A)=Sof(C53A)=Sof(H53A)=Sof(C54A)=Sof(H54A)=Sof(C55A)=
 Sof(H55A)=Sof(C56A)=Sof(H56A)=Sof(C57A)=Sof(H57A)=1-FVAR(1)
 Sof(Pd1)=Sof(H5)=Sof(C51)=Sof(H51)=Sof(C49)=Sof(H49A)=Sof(H49B)=Sof(C50)=
 Sof(H50)=Sof(C52)=Sof(C53)=Sof(H53)=Sof(C54)=Sof(H54)=Sof(C55)=Sof(H55)=
 Sof(C56)=Sof(H56)=Sof(C57)=Sof(H57)=FVAR(1)
3.a Secondary CH2 refined with riding coordinates:
 C58(H58A,H58B), C59(H59A,H59B), C60(H60A,H60B), C61(H61A,H61B), C62(H62A,
 H62B), C63(H63A,H63B), C64(H64A,H64B), C65(H65A,H65B), C66(H66A,H66B),
 C67(H67A,H67B), C68(H68A,H68B), C69(H69A,H69B)
3.b Aromatic/amide H refined with riding coordinates:
 N1(H1), N3(H3), N5(H5), C2(H2), C51(H51), C3(H3A), C7(H7), C8(H8), C12(H12),
 C13(H13), C17(H17), C18(H18), C22(H22), C23(H23), C50(H50), C50A(H50A),
 C51A(H51A), C53(H53), C53A(H53A), C54(H54), C54A(H54A), C55(H55), C55A(H55A),
 C56(H56), C56A(H56A), C57(H57), C57A(H57A)
3.c X=CH2 refined with riding coordinates:
 C49(H49A,H49B), C49A(H49C,H49D)
;
_shelx_res_checksum              65684
_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 1.560
_oxdiff_exptl_absorpt_empirical_full_min 0.716