Atomic-Level Characterization of Dynamics of a 3D Covalent Organic Framework by Cryo-Electron Diffraction Tomography.
Sun, Tu; Wei, Lei; Chen, Yichong; Ma, Yanhang; Zhang, Yue-Biao; Journal of the American Chemical Society 141 (2019) 10962–10966; doi:10.1021/jacs.9b04895

data_4133672
_publ_section_title
;
 Atomic-Level Characterization of Dynamics of a 3D Covalent Organic
 Framework by Cryo-Electron Diffraction Tomography.
;
_journal_issue                   28
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              10962
_journal_page_last               10966
_journal_paper_doi               10.1021/jacs.9b04895
_journal_volume                  141
_journal_year                    2019
_chemical_formula_moiety         '0.25(C164 H112 N16), 4(H2 O)'
_chemical_formula_sum            'C41 H36 N4 O4'
_chemical_formula_weight         648.74
_chemical_name_systematic        COF-300-H2O
_space_group_crystal_system      tetragonal
_space_group_IT_number           88
_space_group_name_Hall           '-I 4ad'
_space_group_name_H-M_alt        'I 41/a :2'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_audit_creation_date             2019-05-05
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   19.900
_cell_length_b                   19.900
_cell_length_c                   9.300
_cell_measurement_temperature    77
_cell_volume                     3682.893
_computing_cell_refinement       &#x00A3;&#x00BF;
_computing_data_collection       'EDT Collect'
_computing_data_reduction        'EDT Process'
_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    'ShelXS (Sheldrick, 2008)'
_diffrn_ambient_temperature      77
_diffrn_measured_fraction_theta_full 0.784
_diffrn_measured_fraction_theta_max 0.784
_diffrn_measurement_device_type  'JEM-2100 Plus with TVIPS CMOS'
_diffrn_radiation_wavelength     0.0251
_diffrn_reflns_av_R_equivalents  0.2979
_diffrn_reflns_av_unetI/netI     0.1769
_diffrn_reflns_Laue_measured_fraction_full 0.784
_diffrn_reflns_Laue_measured_fraction_max 0.784
_diffrn_reflns_limit_h_max       21
_diffrn_reflns_limit_h_min       -21
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -17
_diffrn_reflns_limit_l_max       10
_diffrn_reflns_limit_l_min       -10
_diffrn_reflns_number            3282
_diffrn_reflns_point_group_measured_fraction_full 0.784
_diffrn_reflns_point_group_measured_fraction_max 0.784
_diffrn_reflns_theta_full        0.796
_diffrn_reflns_theta_max         0.796
_diffrn_reflns_theta_min         0.072
_exptl_absorpt_coefficient_mu    0.076
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            'dull light yellow'
_exptl_crystal_colour_lustre     dull
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.170
_exptl_crystal_description       prism
_exptl_crystal_F_000             1368
_exptl_crystal_preparation
'dispersed in water and sonicated, vitrificated in liquid ethane'
_exptl_crystal_recrystallization_method
'Y.-B. Zhang, et al.  J. Am. Chem. Soc. 2019, 141, 3298'
_exptl_crystal_size_max          0.001
_exptl_crystal_size_mid          0.0004
_exptl_crystal_size_min          0.0004
_refine_diff_density_max         0.522
_refine_diff_density_min         -0.501
_refine_diff_density_rms         0.145
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.052
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     114
_refine_ls_number_reflns         1027
_refine_ls_number_restraints     219
_refine_ls_restrained_S_all      0.953
_refine_ls_R_factor_all          0.3074
_refine_ls_R_factor_gt           0.2911
_refine_ls_shift/su_max          0.000
_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^+150.0000P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.6091
_refine_ls_wR_factor_ref         0.6187
_reflns_Friedel_coverage         0.000
_reflns_number_gt                858
_reflns_number_total             1027
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja9b04895_si_004.cif
_cod_data_source_block           COF-300-H2O_cryo
_cod_original_cell_volume        3682.9
_cod_original_sg_symbol_H-M      'I 41/a'
_cod_database_code               4133672
_shelx_shelxl_version_number     2017/1
_shelx_estimated_absorpt_t_max   1.000
_shelx_estimated_absorpt_t_min   1.000
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
 At 1.5 times of:
  All O(H,H) groups
2. Restrained distances
 C2-C4 \\sim C2-C6 \\sim C6-C4 \\sim C3-C7 \\sim C7-C5 \\sim C5-C3 \\sim
C9-C11_$1 \\sim C9-C10_$1 ~
 C10_$1-C11_$1 \\sim C10-C11 \\sim C11-C9_$1 \\sim C9_$1-C10
 with sigma of 0.02
 C3-C2 \\sim C4-C3 \\sim C5-C4 \\sim C6-C5 \\sim C7-C6 \\sim C7-C2 \\sim C9-C11
\\sim C9-C10 \\sim C11_$1-C10
 \\sim C9_$1-C11_$1 \\sim C9_$1-C10_$1 \\sim C11-C10_$1
 with sigma of 0.02
3. Restrained planarity
 C2, C7, C6, C5, C4, C3
 with sigma of 0.1
 C9, C10, C11_$1, C9_$1, C10_$1, C11
 with sigma of 0.1
4. Rigid body (RIGU) restrains
 C11, C9, C8, C10, N1, C5, C4, C3, C2, C7, C6, C1
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5.a Free rotating group:
 O1(H1A,H1B)
5.b Aromatic/amide H refined with riding coordinates:
 C4(H4), C3(H3), C7(H7), C6(H6), C8(H8), C10(H10), C11(H11)
;
_shelx_res_checksum              95824
_shelx_hkl_checksum              45421
_olex2_exptl_crystal_mounting_method
'copper grid coated with ultrathin carbon film'
_olex2_submission_special_instructions 'No special instructions were received'