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#$Date: 2025-04-05 14:35:19 +0300 (Sat, 05 Apr 2025) $
#$Revision: 299174 $
#$URL: file:///home/coder/svn-repositories/cod/cif/2/31/27/2312763.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/. The original data for this entry
# were provided by IUCr Journals, http://journals.iucr.org/.
#
# The file may be used within the scientific community so long as
# proper attribution is given to the journal article from which the
# data were obtained.
#
data_2312763
loop_
_publ_author_name
'Vlahakis, Niko'
'Qu, Songrong'
'Richards, Logan S.'
'Moraes, Lygia Silva de'
'Cascio, Duilio'
'Nelson, Hosea M.'
'Rodriguez, Jose A.'
_publ_section_title
;
 Fast event-based electron counting for small-molecule structure
 determination by MicroED.
;
_journal_coeditor_code           YP3239
_journal_issue                   'Pt 3'
_journal_name_full
'Acta crystallographica. Section C, Structural chemistry'
_journal_page_first              116
_journal_page_last               130
_journal_paper_doi               10.1107/S2053229624012300
_journal_volume                  81
_journal_year                    2025
_chemical_absolute_configuration rm
_chemical_formula_iupac          'C10 H16 N2 O3 S1'
_chemical_formula_moiety         'C10 H16 N2 O3 S1'
_chemical_formula_sum            'C10 H16 N2 O3 S'
_chemical_formula_weight         244.31
_chemical_name_common            biotin
_chemical_name_systematic
;
5-[(3aS,4S,6aR)-2-Oxohexahydro-1H-\
thieno[3,4-d]imidazol-4-yl]pentanoic acid
;
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   geom
_audit_creation_method           SHELXL-2019/3
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   5.170(2)
_cell_length_b                   10.1100(19)
_cell_length_c                   20.710(3)
_cell_measurement_reflns_used    4422
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      0.900
_cell_measurement_theta_min      0.099
_cell_volume                     1082.5(5)
_computing_structure_refinement
;
SHELXL2019 (Sheldrick, 2015b)
;
_computing_structure_solution
;
SHELXT2018 (Sheldrick, 2015a)
;
_diffrn_ambient_temperature      100(2)
_diffrn_measured_fraction_theta_full 0.856
_diffrn_measured_fraction_theta_max 0.847
_diffrn_measurement_device_type  TEM
_diffrn_measurement_method       'continuous rotation 3D ED'
_diffrn_radiation_type           electron
_diffrn_radiation_wavelength     0.0251
_diffrn_reflns_av_R_equivalents  0.1409
_diffrn_reflns_av_unetI/netI     0.1667
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       24
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            4422
_diffrn_reflns_theta_full        0.863
_diffrn_reflns_theta_max         0.900
_diffrn_reflns_theta_min         0.099
_diffrn_source                   FEG
_diffrn_standards_decay_%        0
_diffrn_standards_interval_count 0
_diffrn_standards_interval_time  0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.000
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            white
_exptl_crystal_density_diffrn    1.499
_exptl_crystal_description       needle
_exptl_crystal_F_000             196
_exptl_crystal_size_max          0.010
_exptl_crystal_size_mid          0.0005
_exptl_crystal_size_min          0.00015
_refine_diff_density_max         0.232
_refine_diff_density_min         -0.205
_refine_ls_abs_structure_details
;
 All f" are zero, so absolute structure could not be determined
;
_refine_ls_extinction_coef       1047E1(2)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4^
_refine_ls_extinction_method
;
SHELXL2019 (Sheldrick, 2015b)
;
_refine_ls_goodness_of_fit_ref   1.325
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     148
_refine_ls_number_reflns         1926
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.325
_refine_ls_R_factor_all          0.1856
_refine_ls_R_factor_gt           0.1586
_refine_ls_shift/su_max          0.018
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[σ²(Fo²)+(0.2000P)²] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3832
_refine_ls_wR_factor_ref         0.4094
_reflns_number_gt                1397
_reflns_number_total             1926
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            yp3239.cif
_cod_data_source_block           a
_cod_depositor_comments
'Adding full bibliography for 2312763--2312764.cif.'
_cod_original_formula_sum        'C10 H16 N2 O3 S1'
_cod_database_code               2312763
_shelx_space_group_comment
;
The symmetry employed for this shelxl refinement is uniquely defined
by the following loop, which should always be used as a source of
symmetry information in preference to the above space-group names.
They are only intended as comments.
;
loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x+1/2, -y, z+1/2'
'-x, y+1/2, -z+1/2'
'x+1/2, -y+1/2, -z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_calc_flag
_atom_site_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
S S1 0.4472(12) 0.6291(8) 0.5482(4) 0.056(2) Uani d 1 . .
C C2 0.273(3) 0.6828(15) 0.6642(7) 0.051(4) Uani d 1 . .
H H3 0.156699 0.744934 0.688076 0.061 Uiso calc 1 . .
O O1 0.582(2) 0.4242(13) 0.7461(6) 0.055(3) Uani d 1 . .
C C4 0.395(3) 0.7510(15) 0.6082(8) 0.055(4) Uani d 1 . .
H H5A 0.561126 0.791672 0.621210 0.065 Uiso calc 1 . .
H H5B 0.279576 0.821350 0.591594 0.065 Uiso calc 1 . .
C C5 0.143(2) 0.5560(11) 0.5684(6) 0.034(3) Uani d 1 . .
H H6 0.006644 0.616251 0.550889 0.041 Uiso calc 1 . .
C C3 0.123(2) 0.5632(15) 0.6412(7) 0.047(3) Uani d 1 . .
H H4 -0.061673 0.566286 0.655848 0.056 Uiso calc 1 . .
O O7 0.524(2) 0.5173(13) 0.3109(7) 0.057(3) Uani d 1 . .
H H11 0.704(10) 0.528(2) 0.291(5) 0.085 Uiso calc 1 . .
N N2 0.260(2) 0.4614(12) 0.6715(6) 0.041(3) Uani d 1 . .
H H2 0.222096 0.377591 0.665004 0.049 Uiso calc 1 . .
C C6 0.085(2) 0.4231(13) 0.5432(6) 0.042(3) Uani d 1 . .
H H7A -0.077660 0.392651 0.563801 0.051 Uiso calc 1 . .
H H7B 0.223863 0.362837 0.557680 0.051 Uiso calc 1 . .
C C9 0.252(3) 0.3744(14) 0.3660(8) 0.051(3) Uani d 1 . .
H H10A 0.103149 0.423018 0.347641 0.061 Uiso calc 1 . .
H H10B 0.209890 0.278886 0.365124 0.061 Uiso calc 1 . .
C C1 0.442(2) 0.4973(11) 0.7092(6) 0.034(3) Uani d 1 . .
C C10 0.485(2) 0.3984(14) 0.3245(7) 0.048(4) Uani d 1 . .
N N1 0.463(2) 0.6269(11) 0.7074(6) 0.046(3) Uani d 1 . .
H H1 0.577570 0.673122 0.729473 0.055 Uiso calc 1 . .
C C8 0.290(2) 0.4152(13) 0.4320(7) 0.044(3) Uani d 1 . .
H H9A 0.352328 0.507775 0.432597 0.053 Uiso calc 1 . .
H H9B 0.424798 0.359130 0.451955 0.053 Uiso calc 1 . .
O O00F 0.622(2) 0.3077(14) 0.3020(9) 0.070(4) Uani d 1 . .
C C7 0.054(3) 0.4062(15) 0.4704(7) 0.052(3) Uani d 1 . .
H H8A -0.025508 0.318811 0.462195 0.063 Uiso calc 1 . .
H H8B -0.067987 0.474312 0.454688 0.063 Uiso calc 1 . .
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
N N 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
O O 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
S S 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle
_geom_angle_publ_flag
C4 S1 C5 . . 89.4(7) ?
N1 C2 C4 . . 112.0(12) ?
N1 C2 C3 . . 103.4(11) ?
C4 C2 C3 . . 110.0(13) ?
C2 C4 S1 . . 106.8(11) ?
C6 C5 C3 . . 112.5(10) ?
C6 C5 S1 . . 118.3(9) ?
C3 C5 S1 . . 106.0(9) ?
N2 C3 C5 . . 112.1(12) ?
N2 C3 C2 . . 100.8(10) ?
C5 C3 C2 . . 108.4(10) ?
C1 N2 C3 . . 116.1(12) ?
C5 C6 C7 . . 118.3(12) ?
C8 C9 C10 . . 112.9(11) ?
O1 C1 N2 . . 128.0(13) ?
O1 C1 N1 . . 122.8(11) ?
N2 C1 N1 . . 109.1(11) ?
O00F C10 O7 . . 122.1(13) ?
O00F C10 C9 . . 123.4(13) ?
O7 C10 C9 . . 114.4(11) ?
C1 N1 C2 . . 110.4(11) ?
C9 C8 C7 . . 112.8(11) ?
C8 C7 C6 . . 116.6(12) ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_site_symmetry_2
_geom_bond_distance
_geom_bond_publ_flag
S1 C4 . 1.771(19) ?
S1 C5 . 1.788(13) ?
C2 N1 . 1.446(17) ?
C2 C4 . 1.49(2) ?
C2 C3 . 1.51(2) ?
O1 C1 . 1.285(17) ?
C5 C6 . 1.472(17) ?
C5 C3 . 1.514(19) ?
C3 N2 . 1.398(17) ?
O7 C10 . 1.251(19) ?
N2 C1 . 1.277(16) ?
C6 C7 . 1.53(2) ?
C9 C8 . 1.44(2) ?
C9 C10 . 1.500(18) ?
C1 N1 . 1.316(17) ?
C10 O00F . 1.247(19) ?
C8 C7 . 1.46(2) ?
