Biomimetic mimicry of formaldehyde-induced DNA–protein crosslinks in the confined space of a metal–organic framework
Wei, Yu-Bai; Luo, Dong; Xiong, Xiao; Huang, Yong-Liang; Xie, Mo; Lu, Weigang; Li, Dan; Chemical Science 13 (2022) 4813–4820; doi:10.1039/D2SC00188H

data_1566908
_publ_section_title
;
 Biomimetic mimicry of formaldehyde-induced DNA--protein crosslinks in the
 confined space of a metal--organic framework
;
_journal_issue                   17
_journal_name_full               'Chemical Science'
_journal_page_first              4813
_journal_page_last               4820
_journal_paper_doi               10.1039/D2SC00188H
_journal_volume                  13
_journal_year                    2022
_chemical_formula_moiety         '0.5(C132 H100 N60 O30 Zn12)'
_chemical_formula_sum            'C66 H50 N30 O15 Zn6'
_chemical_formula_weight         1895.58
_space_group_crystal_system      monoclinic
_space_group_IT_number           13
_space_group_name_Hall           '-P 2yc'
_space_group_name_H-M_alt        'P 1 2/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2020-10-10
_audit_creation_method
;
Olex2 1.2-beta
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2021-08-11 deposited with the CCDC.	2022-04-07 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 94.526(6)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   20.5389(19)
_cell_length_b                   15.2128(5)
_cell_length_c                   21.6422(9)
_cell_measurement_reflns_used    4987
_cell_measurement_temperature    100.00(18)
_cell_measurement_theta_max      68.6560
_cell_measurement_theta_min      3.5260
_cell_volume                     6741.1(7)
_computing_cell_refinement       'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_computing_data_collection       'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_computing_data_reduction        'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(18)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.971
_diffrn_measured_fraction_theta_max 0.971
_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     20.00  55.00   0.50    4.50    --    0.00  71.00 167.00   70
  2  \w    -44.00  -9.00   0.50    4.50    --    0.00 -71.00  37.00   70
  3  \w     37.00  62.00   0.50   40.00    --   90.80 -71.00  37.00   50
  4  \w    118.00 146.00   0.50   40.00    --   90.80  71.00 167.00   56
  5  \w    -20.00  37.00   0.50    4.50    --    0.00  82.00  60.00  114
  6  \w    -26.00  38.00   0.50    4.50    --    0.00  82.00-150.00  128
  7  \w     81.00 179.00   0.50   40.00    --   90.80  82.00 150.00  196
  8  \w     35.00 123.00   0.50   40.00    --   90.80 -77.00  60.00  176
  9  \w     69.00 176.00   0.50   40.00    --   90.80  57.00 -90.00  214
 10  \w     65.00 180.00   0.50   40.00    --   90.80  57.00-120.00  230
 11  \w    136.00 180.00   0.50   40.00    --   90.80  77.00-150.00   88
 12  \w     79.00 104.00   0.50   40.00    --   90.80  77.00-150.00   50
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC12 (RINC): Kappa single'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0708825000
_diffrn_orient_matrix_UB_12      -0.0177843000
_diffrn_orient_matrix_UB_13      0.0257733000
_diffrn_orient_matrix_UB_21      -0.0033280000
_diffrn_orient_matrix_UB_22      0.0789871000
_diffrn_orient_matrix_UB_23      0.0441179000
_diffrn_orient_matrix_UB_31      -0.0252285000
_diffrn_orient_matrix_UB_32      -0.0607476000
_diffrn_orient_matrix_UB_33      0.0498320000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0519
_diffrn_reflns_av_unetI/netI     0.0543
_diffrn_reflns_Laue_measured_fraction_full 0.971
_diffrn_reflns_Laue_measured_fraction_max 0.971
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -22
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       25
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            31357
_diffrn_reflns_point_group_measured_fraction_full 0.971
_diffrn_reflns_point_group_measured_fraction_max 0.971
_diffrn_reflns_theta_full        63.999
_diffrn_reflns_theta_max         63.999
_diffrn_reflns_theta_min         2.905
_diffrn_source                   'Rotating-anode X-ray tube (dual wavelength)'
_diffrn_source_type              'Rigaku (Cu) X-ray DW Source'
_exptl_absorpt_coefficient_mu    1.586
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.37327
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.33c (Rigaku Oxford Diffraction, 2017)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    0.934
_exptl_crystal_description       plate
_exptl_crystal_F_000             1912
_exptl_crystal_size_max          0.42
_exptl_crystal_size_mid          0.3
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.898
_refine_diff_density_min         -0.420
_refine_diff_density_rms         0.099
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.058
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     558
_refine_ls_number_reflns         10879
_refine_ls_number_restraints     817
_refine_ls_restrained_S_all      1.096
_refine_ls_R_factor_all          0.1574
_refine_ls_R_factor_gt           0.1162
_refine_ls_shift/su_max          0.005
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2985
_refine_ls_wR_factor_ref         0.3476
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4706
_reflns_number_total             10879
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2sc00188h2.cif
_cod_data_source_block           5_HCHO_JNU_101
_cod_database_code               1566908
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.925
_shelx_estimated_absorpt_t_min   0.556
_reflns_odcompleteness_completeness 99.13
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     63.60
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups, All N(H,H) groups
2. Restrained distances
 O7-C13 = C13-O5
 1.22 with sigma of 0.02
 O5-O7
 2.22 with sigma of 0.02
 C19-C13
 1.52 with sigma of 0.02
 O10-C39 = C39-O9
 1.22 with sigma of 0.02
 O6-O8 = O10-O9
 2.22 with sigma of 0.02
 O6-C32 = C32-O8
 1.22 with sigma of 0.02
 O8-O6
 2.22 with sigma of 0.02
 C30-C33
 1.5 with sigma of 0.02
 C36-C39 = C27-C32
 1.52 with sigma of 0.02
 N16-C38 = C29-N15
 1.35 with sigma of 0.02
 N14-C20
 1.35 with sigma of 0.02
 O6-O8
 2.22 with sigma of 0.01
 O8-C32 = C32-O6
 1.22 with sigma of 0.01
 C33-C30
 1.5 with sigma of 0.02
 O7-C19 \\sim C19-O5
 with sigma of 0.02
 C18-C13 \\sim C13-C14
 with sigma of 0.02
 O6-C27 \\sim C27-O8
 with sigma of 0.02
 C28-C32 \\sim C32-C26
 with sigma of 0.02
 C28-N15 \\sim N15-C30
 with sigma of 0.02
 C26-C32 \\sim C32-C28
 with sigma of 0.02
 O8-C27 \\sim C27-O6
 with sigma of 0.02
 C33-N16 \\sim N16-C37
 with sigma of 0.02
 O9-C36 \\sim C36-O10
 with sigma of 0.02
 C35-C39 \\sim C39-C37
 with sigma of 0.02
 C29-C38 \\sim C31-C34
 with sigma of 0.02
 N14-C40 \\sim C40-N13
 with sigma of 0.02
3. Restrained planarity
 O7, C13, O5, C19
 with sigma of 0.01
 C28, C29, C30, N15
 with sigma of 0.01
 O6, O8, C27, C32
 with sigma of 0.01
 C28, C27, C32, C26
 with sigma of 0.01
 C29, C30, C31, C33
 with sigma of 0.01
 O9, O10, C39, C36
 with sigma of 0.01
 C39, C36, C35, C37
 with sigma of 0.01
4. Rigid bond restraints
 O6, O8, C26, C27, C28, C29, C30, C31, C32, N15, O9, O10, C33, C34, C35, C36,
 C37, C38, C39, N16
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.01
 O2, O3, O5, C1, N13, C13, C14, C15, C16, C17, C18, C19, C20, C21, C22, C23,
 C24, C25, N14, O7, C40
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.01
5. Uiso/Uaniso restraints and constraints
O6 \\sim O8 \\sim C26 \\sim C27 \\sim C28 \\sim C29 \\sim C30 \\sim C31 \\sim
C32 \\sim N15 \\sim O9 \\sim O10 \\sim C33 \\sim C34 \\sim C35 \\sim C36 \\sim
C37 \\sim C38 \\sim C39 \\sim N16: within 1.7A with sigma of 0.02 and sigma for
terminal atoms of 0.04
O2 \\sim O3 \\sim O5 \\sim C1 \\sim N13 \\sim C13 \\sim C14 \\sim C15 \\sim C16
\\sim C17 \\sim C18 \\sim C19 \\sim C20 \\sim C21 \\sim C22 \\sim C23 \\sim C24
\\sim C25 \\sim N14 \\sim O7 \\sim C40: within 1.7A with sigma of 0.02 and
sigma for terminal atoms of 0.04
Uanis(O6) \\sim Ueq, Uanis(O8) \\sim Ueq, Uanis(C26) \\sim Ueq, Uanis(C27)
\\sim Ueq, Uanis(C28) \\sim Ueq, Uanis(C29) \\sim Ueq, Uanis(C30) \\sim Ueq,
Uanis(C31) \\sim Ueq, Uanis(C32) \\sim Ueq, Uanis(N15) \\sim Ueq, Uanis(O9)
\\sim Ueq, Uanis(O10) \\sim Ueq, Uanis(C33) \\sim Ueq, Uanis(C34) \\sim Ueq,
Uanis(C35) \\sim Ueq, Uanis(C36) \\sim Ueq, Uanis(C37) \\sim Ueq, Uanis(C38)
\\sim Ueq, Uanis(C39) \\sim Ueq, Uanis(N16) \\sim Ueq: with sigma of 0.03 and
sigma for terminal atoms of 0.1
Uanis(O2) \\sim Ueq, Uanis(O3) \\sim Ueq, Uanis(O5) \\sim Ueq, Uanis(C1) \\sim
Ueq, Uanis(C13) \\sim Ueq, Uanis(C14) \\sim Ueq, Uanis(C15) \\sim Ueq,
Uanis(C16) \\sim Ueq, Uanis(C17) \\sim Ueq, Uanis(C18) \\sim Ueq, Uanis(C19)
\\sim Ueq, Uanis(C20) \\sim Ueq, Uanis(C21) \\sim Ueq, Uanis(C22) \\sim Ueq,
Uanis(C23) \\sim Ueq, Uanis(C24) \\sim Ueq, Uanis(C25) \\sim Ueq, Uanis(O7)
\\sim Ueq, Uanis(N13) \\sim Ueq, Uanis(C40) \\sim Ueq, Uanis(N14) \\sim Ueq:
with sigma of 0.03 and sigma for terminal atoms of 0.1
6. Rigid body (RIGU) restrains
 O6, O8, C26, C27, C28, C29, C30, C31, C32, N15, O9, O10, C33, C34, C35, C36,
 C37, C38, C39, N16
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 N13, C40, N14
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
7. Others
 Fixed Sof: O6(0.5) O8(0.5) C26(0.5) H26(0.5) C27(0.5) C28(0.5) H28(0.5)
 C29(0.5) C30(0.5) C31(0.5) H31(0.5) C32(0.5) N15(0.5) H15A(0.5) H15B(0.5)
 O9(0.5) O10(0.5) C33(0.5) C34(0.5) H34(0.5) C35(0.5) H35(0.5) C36(0.5)
 C37(0.5) H37(0.5) C38(0.5) C39(0.5) N16(0.5) H16A(0.5) H16B(0.5)
8.a Secondary CH2 refined with riding coordinates:
 C12(H12C,H12D), C40(H40A,H40B)
8.b Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), N9(H9), C14(H14), C17(H17), C18(H18), C21(H21), C23(H23),
 C24(H24), N14(H14A), C26(H26), C28(H28), C31(H31), C34(H34), C35(H35), C37(H37)
8.c Fitted hexagon refined as free rotating group:
 C7(N10,C8,N11,C9,C10), C14(C15,C16,C17,C18,C19), C20(C21,C22,C23,C24,C25),
 C26(C27,C28,C29,C30,C31), C33(C34,C35,C36,C37,C38)
8.d X=CH2 refined with riding coordinates:
 N5(H5A,H5B), N8(H8A,H8B), N12(H12A,H12B), N15(H15A,H15B), N16(H16A,H16B)
;
_shelx_res_checksum              15098
_shelx_fab_checksum              81577
_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 3.130
_oxdiff_exptl_absorpt_empirical_full_min 0.585