#------------------------------------------------------------------------------
#$Date: 2025-02-11 05:41:48 +0200 (Tue, 11 Feb 2025) $
#$Revision: 297679 $
#$URL: file:///home/coder/svn-repositories/cod/cif/1/57/38/1573874.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_1573874
loop_
_publ_author_name
'Vlahakis, Niko'
'Clauss, Arden'
'Rodriguez, Jose A.'
_publ_section_title
;
 Accounting for electron-beam-induced warping of molecular nanocrystals in
 MicroED structure determination.
;
_journal_coeditor_code           NF5001SUP1
_journal_issue                   2
_journal_name_full               IUCrJ
_journal_paper_doi               10.1107/S2052252524012132
_journal_volume                  12
_journal_year                    2025
_chemical_absolute_configuration rm
_chemical_formula_sum            'C12 H24 Cu2 N4 O12'
_chemical_formula_weight         543.43
_chemical_name_common            Cu(II)-serine
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_method           SHELXL-2019/3
_audit_update_record
;
2024-04-12 # Formatted by publCIF

;
_cell_angle_alpha                90
_cell_angle_beta                 90.33
_cell_angle_gamma                90
_cell_formula_units_Z            1
_cell_length_a                   5.510(2)
_cell_length_b                   8.2400(19)
_cell_length_c                   9.720(3)
_cell_measurement_reflns_used    3266
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      0.898
_cell_measurement_theta_min      0.114
_cell_volume                     441.3(2)
_computing_structure_refinement  'SHELXL-2019/2 (Sheldrick, 2019)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      100(2)
_diffrn_measured_fraction_theta_full 0.896
_diffrn_measured_fraction_theta_max 0.882
_diffrn_measurement_device_type  TEM
_diffrn_radiation_type           Electron
_diffrn_radiation_wavelength     0.0251
_diffrn_reflns_av_R_equivalents  0.1191
_diffrn_reflns_av_unetI/netI     0.1657
_diffrn_reflns_Laue_measured_fraction_full 0.896
_diffrn_reflns_Laue_measured_fraction_max 0.882
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       10
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       11
_diffrn_reflns_limit_l_min       -11
_diffrn_reflns_number            3266
_diffrn_reflns_point_group_measured_fraction_full 0.903
_diffrn_reflns_point_group_measured_fraction_max 0.887
_diffrn_reflns_theta_full        0.863
_diffrn_reflns_theta_max         0.898
_diffrn_reflns_theta_min         0.114
_diffrn_source                   FEG
_exptl_absorpt_coefficient_mu    0.000
_exptl_crystal_colour            Blue
_exptl_crystal_density_diffrn    2.045
_exptl_crystal_description       Plate
_exptl_crystal_F_000             87
_refine_diff_density_max         0.272
_refine_diff_density_min         -0.230
_refine_diff_density_rms         0.060
_refine_ls_abs_structure_details
;
 All f" are zero, so absolute structure could not be determined
;
_refine_ls_extinction_coef       33452(35)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2019/2 (Sheldrick 2019)'
_refine_ls_goodness_of_fit_ref   1.125
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     141
_refine_ls_number_reflns         1584
_refine_ls_number_restraints     217
_refine_ls_restrained_S_all      1.056
_refine_ls_R_factor_all          0.1357
_refine_ls_R_factor_gt           0.1217
_refine_ls_shift/su_max          0.013
_refine_ls_shift/su_mean         0.001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[σ²(Fo²)+(0.1796P)²+0.2784P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3225
_refine_ls_wR_factor_ref         0.3441
_reflns_Friedel_coverage         0.877
_reflns_Friedel_fraction_full    0.912
_reflns_Friedel_fraction_max     0.893
_reflns_number_gt                1366
_reflns_number_total             1584
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            nf5001.cif
_cod_data_source_block           CuIIserine
_cod_original_sg_symbol_H-M      'P 21'
_cod_database_code               1573874
_shelx_shelxl_version_number     2019/3
_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.
;
_publcif_funding_html
;
;
loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x, y+1/2, -z'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
_atom_site_site_symmetry_order
_atom_site_calc_flag
_atom_site_refinement_flags_posn
_atom_site_refinement_flags_adp
_atom_site_refinement_flags_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
O5 O 0.277(2) 0.3122(17) 0.6169(18) 0.0154(14) Uani 1 1 d . U . . .
Cu1 Cu 0.4851(9) 0.5927(10) 0.3191(6) 0.0151(10) Uani 1 1 d . U . . .
O6 O 0.504(2) 0.4388(17) 0.4682(18) 0.0152(11) Uani 1 1 d . U . . .
O3 O 0.760(2) 0.4872(16) 0.2352(18) 0.0155(11) Uani 1 1 d . U . . .
O2 O 1.015(2) 0.5040(17) 0.0733(17) 0.0170(17) Uani 1 1 d . U . . .
O1 O 0.548(3) 0.5409(17) -0.1228(19) 0.0167(18) Uani 1 1 d . U . . .
H1 H 0.429(17) 0.567(4) -0.166(11) 0.025 Uiso 1 1 calc R U . . .
C6 C 0.3157(9) 0.4204(6) 0.5330(16) 0.0152(12) Uani 1 1 d D U . . .
C2 C 0.6866(12) 0.6899(5) 0.0742(3) 0.0156(13) Uani 1 1 d D U . . .
H3 H 0.773597 0.791963 0.100352 0.019 Uiso 1 1 calc R U . . .
N1 N 0.451(3) 0.6935(19) 0.1325(19) 0.0155(14) Uani 1 1 d . U . . .
H4A H 0.344719 0.636000 0.079721 0.019 Uiso 1 1 calc R U . . .
H4B H 0.396773 0.797432 0.139542 0.019 Uiso 1 1 calc R U . . .
C5 C 0.1159(8) 0.5417(4) 0.5056(5) 0.0152(12) Uani 1 1 d D U . . .
H7 H -0.021092 0.486739 0.456385 0.018 Uiso 1 1 calc R U . . .
C3 C 0.8323(13) 0.5469(5) 0.1257(11) 0.0157(12) Uani 1 1 d D U . . .
N2 N 0.207(2) 0.6701(18) 0.4225(18) 0.0150(11) Uani 1 1 d . U . . .
H8A H 0.251883 0.755120 0.476742 0.018 Uiso 1 1 calc R U . . .
H8B H 0.089089 0.704899 0.363551 0.018 Uiso 1 1 calc R U . . .
O4 O 0.209(2) 0.6755(18) 0.7200(17) 0.0166(18) Uani 1 1 d . U . . .
H5 H 0.187(10) 0.786(12) 0.724(8) 0.025 Uiso 1 1 calc R U . . .
C1 C 0.673(3) 0.680(2) -0.0807(4) 0.0158(14) Uani 1 1 d D U . . .
H2A H 0.588846 0.777502 -0.117003 0.019 Uiso 1 1 calc R U . . .
H2B H 0.839181 0.678595 -0.118831 0.019 Uiso 1 1 calc R U . . .
C4 C 0.0271(18) 0.6070(11) 0.6414(5) 0.0156(13) Uani 1 1 d D U . . .
H6A H -0.099730 0.689613 0.623690 0.019 Uiso 1 1 calc R U . . .
H6B H -0.048253 0.517442 0.694005 0.019 Uiso 1 1 calc R U . . .
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'
Cu Cu 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
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
C6 O5 Cu1 130.2(9) . 2_646 ?
O6 Cu1 O3 89.0(6) . . ?
O6 Cu1 N2 82.3(6) . . ?
O3 Cu1 N2 171.1(7) . . ?
O6 Cu1 N1 163.3(6) . . ?
O3 Cu1 N1 82.8(7) . . ?
N2 Cu1 N1 105.2(7) . . ?
O6 Cu1 O5 106.5(7) . 2_656 ?
O3 Cu1 O5 91.2(5) . 2_656 ?
N2 Cu1 O5 93.0(6) . 2_656 ?
N1 Cu1 O5 88.2(6) . 2_656 ?
C6 O6 Cu1 115.3(11) . . ?
C3 O3 Cu1 116.0(9) . . ?
O6 C6 O5 125.6(10) . . ?
O6 C6 C5 116.4(11) . . ?
O5 C6 C5 117.9(9) . . ?
N1 C2 C3 111.7(8) . . ?
N1 C2 C1 111.0(10) . . ?
C3 C2 C1 108.2(8) . . ?
C2 N1 Cu1 105.8(9) . . ?
N2 C5 C4 110.4(8) . . ?
N2 C5 C6 109.5(7) . . ?
C4 C5 C6 108.8(7) . . ?
O2 C3 O3 121.8(11) . . ?
O2 C3 C2 122.8(10) . . ?
O3 C3 C2 115.0(9) . . ?
C5 N2 Cu1 109.3(8) . . ?
O1 C1 C2 110.9(11) . . ?
O4 C4 C5 113.1(9) . . ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
O5 C6 1.228(19) . ?
O5 Cu1 2.317(14) 2_646 ?
Cu1 O6 1.928(16) . ?
Cu1 O3 1.933(14) . ?
Cu1 N2 1.945(14) . ?
Cu1 N1 2.002(19) . ?
O6 C6 1.224(17) . ?
O3 C3 1.240(18) . ?
O2 C3 1.185(15) . ?
O1 C1 1.40(2) . ?
C6 C5 1.510(4) . ?
C2 N1 1.419(15) . ?
C2 C3 1.510(4) . ?
C2 C1 1.510(4) . ?
C5 N2 1.424(16) . ?
C5 C4 1.510(4) . ?
O4 C4 1.376(18) . ?
loop_
_publcif_info_cif.paper_type
?
