Kawamoto, Akihiro; Kojima Chojiro; Kurisu, Genji; Nakane, Takanori; Nakatani Kazuhiko; Sakurabayashi Shuhei; Journal of the American Chemical Society  (2025) –; doi:10.1021/jacs.4c17538

data_3000497
_journal_name_full               'Journal of the American Chemical Society'
_journal_paper_doi               10.1021/jacs.4c17538
_journal_year                    2025
_chemical_formula_moiety         '3(Cl), C24 H26 N7 O2, 3(O)'
_chemical_formula_sum            'C24 H26 Cl3 N7 O5'
_chemical_formula_weight         598.88
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     iterative
_audit_creation_date             2024-03-28
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_cell_angle_alpha                90
_cell_angle_beta                 91.41
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   7.078
_cell_length_b                   11.743
_cell_length_c                   34.698
_cell_measurement_reflns_used    163450
_cell_measurement_temperature    79
_cell_measurement_theta_max      0.903914139384784
_cell_measurement_theta_min      0.12005553682119431
_cell_volume                     2883.119
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/2 (Sheldrick, 2015)'
_computing_structure_solution    'olex2.solve 1.5 (Bourhis et al., 2015); SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      79
_diffrn_measured_fraction_theta_full 0.981
_diffrn_measured_fraction_theta_max 0.981
_diffrn_measurement_device_type  'Talos Arctica'
_diffrn_radiation_type           electron
_diffrn_radiation_wavelength     0.02508
_diffrn_reflns_av_R_equivalents  0.3596
_diffrn_reflns_av_unetI/netI     0.1078
_diffrn_reflns_Laue_measured_fraction_full 0.981
_diffrn_reflns_Laue_measured_fraction_max 0.981
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       42
_diffrn_reflns_limit_l_min       -42
_diffrn_reflns_number            1195981
_diffrn_reflns_point_group_measured_fraction_full 0.981
_diffrn_reflns_point_group_measured_fraction_max 0.981
_diffrn_reflns_theta_full        0.862
_diffrn_reflns_theta_max         0.898
_diffrn_reflns_theta_min         0.119
_diffrn_source                   'Talos Arctica'
_exptl_absorpt_coefficient_mu    0.000
_exptl_crystal_colour            'clear whiteish colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   whiteish
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.380
_exptl_crystal_description       needle
_exptl_crystal_F_000             446
_refine_diff_density_max         0.612
_refine_diff_density_min         -0.340
_refine_diff_density_rms         0.130
_refine_ls_extinction_coef       90153(9)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2019/2 (Sheldrick 2019)'
_refine_ls_goodness_of_fit_ref   2.722
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     355
_refine_ls_number_reflns         5786
_refine_ls_number_restraints     483
_refine_ls_restrained_S_all      2.624
_refine_ls_R_factor_all          0.2307
_refine_ls_R_factor_gt           0.2149
_refine_ls_wR_factor_ref         0.5835
_refine_ls_shift/su_max          0.019
_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          0.5817
_reflns_Friedel_coverage         0.000
_reflns_Friedel_fraction_full    .
_reflns_Friedel_fraction_max     .
_reflns_number_gt                4647
_reflns_number_total             5786
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            NDcod2.cif
_cod_data_source_block           nd
_cod_original_cell_volume        2882.9
_cod_database_code               3000497
_shelx_shelxl_version_number     2019/2
_diffrn_oxdiff_scatteringfactors_ed 'CAP prior to 43.51a'
  _refine_ls_R_factor_gt             0.2149
  _refine_ls_wR_factor_ref           0.5835

The authors of this entry reported in their 2024-04-24 09:38 EEST
e-mail:

This is a MicroED structure refined only kinematically.

Thus, traditional X-ray crystallography thresholds are not adequate.
;
'Saulius Gra\<zulis' 2024-04-24
_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
 At 1.5 times of:
  All C(H,H,H) groups
2. Uiso/Uaniso restraints and constraints
N3 \\sim C10 \\sim C9 \\sim O1 \\sim C11 \\sim N2 \\sim C8 \\sim C12 \\sim C6
\\sim C7 \\sim N4 \\sim C5 \\sim N1 \\sim C13 \\sim C14 \\sim C4 \\sim C2 \\sim
C15 \\sim C3 \\sim C1 \\sim N5 \\sim O2 \\sim C16 \\sim N6 \\sim C17 \\sim C20
\\sim C18 \\sim N7 \\sim C19 \\sim C23 \\sim C21 \\sim C22 \\sim C24: within
1.7A with sigma of 0.005 and sigma for terminal atoms of 0.01 within 1.7A
Uanis(O4) \\sim Ueq: with sigma of 0.05 and sigma for terminal atoms of 0.1
Uanis(Cl) \\sim Ueq: with sigma of 0.05 and sigma for terminal atoms of 0.1
3. Rigid body (RIGU) restrains
 C5, O2, C15, N5, C14, C16, C13, N6, C17, N4, C20, C18, C12, N7, C19, C11, C23,
  C21, C10, C22, C24, N3, O1, C9, N2, C8, C6, C7, N1, C4, C2, C3, C1
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
4.a Secondary CH2 refined with riding coordinates:
 C13(H13A,H13B), N4(H4A,H4B), C12(H12A,H12B), C14(H14A,H14B), C11(H11A,H11B)
4.b Aromatic/amide H refined with riding coordinates:
 N3(H3), C17(H17), N5(H5), C4(H4), C22(H22), C7(H7), C18(H18), C3(H3A),
 C21(H21), C8(H8)
4.c Idealised Me refined as rotating group:
 C24(H24A,H24B,H24C), C1(H1A,H1B,H1C)
;
_shelx_res_checksum              49750

_shelx_hkl_checksum              80383
_olex2_submission_special_instructions 'No special instructions were received'