HAR, TAAM and BODD refinements of model crystal structures using Cu~<i>K</i>α and Mo~<i>K</i>α X-ray diffraction data
Wanat, Monika; Malinska, Maura; Gutmann, Matthias J.; Cooper, Richard I.; Wozniak, Krzysztof; Acta Crystallographica Section B 77 (2021) –; doi:10.1107/S2052520620014936

data_2108759
_publ_section_title
;
 HAR, TAAM and BODD refinements of model crystal structures using
 Cu~<i>K</i>\a and Mo~<i>K</i>\a X-ray diffraction data
;
_journal_issue                   1
_journal_name_full               'Acta Crystallographica Section B'
_journal_page_first
;
;
_journal_paper_doi               10.1107/S2052520620014936
_journal_volume                  77
_journal_year                    2021
_chemical_formula_iupac          'C5 H6 N2 O2'
_chemical_formula_moiety         'C5 H6 N2 O2'
_chemical_formula_sum            'C5 H6 N2 O2'
_chemical_formula_weight         126.12
_chemical_name_common            Methyluracil
_chemical_name_systematic
;
1-Methylpyrimidine-2,4(1<i>H</i>,3<i>H</i>)-dione
;
_space_group_crystal_system      orthorhombic
_space_group_IT_number           72
_space_group_name_Hall           '-I 2 2c'
_space_group_name_H-M_alt        'I b a m'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2018-02-26
_audit_creation_method
;
Olex2 1.2
(compiled 2017.08.10 svn.r3458 for OlexSys, GUI svn.r5381)
;
_audit_update_record
;
2020-12-02 # Formatted by IUCr publCIF

;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   13.17921(17)
_cell_length_b                   13.20059(19)
_cell_length_c                   6.21502(11)
_cell_measurement_reflns_used    13558
_cell_measurement_temperature    123.00(10)
_cell_measurement_theta_max      75.2890
_cell_measurement_theta_min      4.6970
_cell_volume                     1081.25(3)
_computing_cell_refinement
;
CrysAlis PRO (Agilent, 2014)
;
_computing_data_collection
;
CrysAlis PRO (Agilent, 2014)
;
_computing_data_reduction
;
CrysAlis PRO (Agilent, 2014)
;
_computing_molecular_graphics    'OLEX2 (Dolomanov et al., 2009)'
_computing_publication_material  'OLEX2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL2014 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXS97 (Sheldrick, 2008)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      123.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2195
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_details
;
  1 omega    1.00   51.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -        0.0000  -99.0000  -90.0000 50

  2 omega  -47.00   91.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -        0.0000   37.0000   90.0000 138

  3 omega -100.00   44.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -        0.0000  -77.0000   60.0000 144

  4 omega  -31.00    0.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       34.0000  123.0000  -50.8794 31

  5 omega  -11.00   17.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       42.0000  104.0000  132.1370 28

  6 omega    2.00   28.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       50.0000   92.0000   57.9478 26

  7 omega    1.00   27.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       50.0000   93.0000 -173.0430 26

  8 omega -103.00   32.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -      -60.5000   61.0000   90.0000 135

  9 omega -152.00  -73.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -      -60.5000 -125.0000    0.0000 79

 10 omega   17.00   49.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000   78.0000   65.3098 32

 11 omega   94.00  152.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000  125.0000   60.0000 58

 12 omega   16.00   45.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000   82.0000   12.7628 29

 13 omega   23.00  121.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000 -125.0000  -60.0000 98

 14 omega   17.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000   77.0000  120.0000 144

 15 omega   17.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000   77.0000  -90.0000 144

 16 omega   17.00   47.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000   79.0000 -144.3742 30

 17 omega   19.00  159.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       62.0000   70.0000  -13.0843 140

 18 omega   23.00  164.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       66.0000   73.0000  -44.8045 141

 19 omega   26.00  164.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       70.0000   65.0000   62.5920 138

 20 omega   28.00  162.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       70.0000   58.0000    6.5503 134

 21 omega   31.00  169.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       74.0000   67.0000  167.1024 138

 22 omega   34.00  172.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       78.0000   65.0000  104.0512 138

 23 omega   39.00  178.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       82.0000   73.0000 -165.5957 139

 24 omega   47.00  178.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       90.0000   70.0000  -61.6672 131

 25 omega   47.00  178.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       90.0000   73.0000  -96.7270 131

 26 omega   50.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -       94.0000   63.0000 -106.7252 128

 27 omega   55.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -       98.0000   74.0000  156.3812 123

 28 omega   55.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -       98.0000   43.0000   31.3402 123

 29 omega   78.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   73.0000  175.0000 100

 30 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   63.0000  -90.0000 101

 31 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   63.0000 -120.0000 101

 32 omega   79.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   50.0000   90.0000 99

 33 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   63.0000   30.0000 101

 34 omega   24.00  169.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000  -91.0000  150.0000 145

 35 omega   29.00  115.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000 -111.0000    0.0000 86

 36 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   63.0000   60.0000 101

 37 omega   57.00  150.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000  178.0000  150.0000 93

 38 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   77.0000    0.0000 101

 39 omega   29.00  115.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000 -111.0000  120.0000 86

 40 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   77.0000  -60.0000 101

 41 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   77.0000  -90.0000 101

 42 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   77.0000  -30.0000 101

 43 omega   29.00  115.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000 -111.0000 -120.0000 86

 44 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   63.0000 -150.0000 101

 45 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   63.0000    0.0000 101

 46 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   63.0000   90.0000 101

 47 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   77.0000  150.0000 101

 48 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   77.0000   90.0000 101

 49 omega  100.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000  111.0000  -60.0000 78

 50 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   63.0000  150.0000 101

 51 omega   30.00  163.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000  -50.0000 -150.0000 133

 52 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   63.0000  -60.0000 101

 53 omega  100.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000  111.0000 -120.0000 78

 54 omega   24.00  169.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000  -91.0000 -120.0000 145

 55 omega   77.00  178.00   1.0000    3.0000
omega____ theta____ kappa____ phi______ frames
    -      121.0000   63.0000  120.0000 101

 56 omega -100.00  100.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -        0.0000    0.0000 -180.0000 200

 57 omega -100.00  100.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -        0.0000    0.0000 -120.0000 200

 58 omega    1.00   51.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -        0.0000  -99.0000    0.0000 50

 59 omega -100.00  100.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -        0.0000    0.0000 -150.0000 200

 60 omega -159.00  -17.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -      -60.5000  -73.0000   46.0000 142

 61 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000  -90.0000 201

 62 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000 -150.0000 201

 63 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000  120.0000 201

 64 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000 -180.0000 201

 65 omega   94.00  152.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000  125.0000  -60.0000 58

 66 omega  -40.00  106.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000  150.0000 146

 67 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000 -120.0000 201

 68 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000   30.0000 201

 69 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000  -60.0000 201

 70 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000    0.0000 201

 71 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000  -30.0000 201

 72 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000   90.0000 201

 73 omega  -40.00  161.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       60.5000    0.0000   60.0000 201

 74 omega   22.00  166.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       66.0000   77.0000    2.6493 144

 75 omega   28.00  162.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       70.0000   58.0000  162.6499 134

 76 omega   32.00  166.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       74.0000   58.0000  -95.0200 134

 77 omega   47.00  178.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       90.0000   61.0000  174.1981 131
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type
'Agilent SuperNova Dual four-circle diffractometer with an Atlas detector'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_UB_11      -0.1100741000
_diffrn_orient_matrix_UB_12      0.0341433000
_diffrn_orient_matrix_UB_13      0.0405286000
_diffrn_orient_matrix_UB_21      -0.0145974000
_diffrn_orient_matrix_UB_22      -0.0887824000
_diffrn_orient_matrix_UB_23      0.1578569000
_diffrn_orient_matrix_UB_31      0.0363686000
_diffrn_orient_matrix_UB_32      0.0676290000
_diffrn_orient_matrix_UB_33      0.1868846000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0465
_diffrn_reflns_av_unetI/netI     0.0262
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       16
_diffrn_reflns_limit_k_min       -16
_diffrn_reflns_limit_l_max       7
_diffrn_reflns_limit_l_min       -7
_diffrn_reflns_number            627
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         75.522
_diffrn_reflns_theta_min         4.741
_diffrn_source                   'sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.041
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.50496
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
(CrysAlis PRO; Agilent, 2014)
;
_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    1.549
_exptl_crystal_description       needle
_exptl_crystal_F_000             528
_exptl_crystal_size_max          0.31
_exptl_crystal_size_mid          0.07
_exptl_crystal_size_min          0.04
_refine_diff_density_max         0.310
_refine_diff_density_min         -0.283
_refine_diff_density_rms         0.050
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.095
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     62
_refine_ls_number_reflns         627
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.095
_refine_ls_R_factor_all          0.0347
_refine_ls_R_factor_gt           0.0336
_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^)+(0.0647P)^2^+0.5188P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1020
_refine_ls_wR_factor_ref         0.1042
_reflns_Friedel_coverage         0.000
_reflns_number_gt                599
_reflns_number_total             627
_reflns_threshold_expression     'I > 2\s(I)'
_publcif_datablock.id            {3feb8569-64e9-48f7-896c-e27cd7936c1b}
_cod_data_source_file            px5028sup1.cif
_cod_data_source_block           3Cu
_cod_database_code               2108759
_cod_database_fobs_code          2108759
_shelx_shelxl_version_number     2016/4
_chemical_oxdiff_formula         C5H6N2O2
_chemical_oxdiff_usercomment     '123 K'
_shelx_estimated_absorpt_t_max   0.960
_shelx_estimated_absorpt_t_min   0.738
_exptl_absorpt_special_details
;
CrysAlisPro, Agilent Technologies,
Version 1.171.37.34 (release 22-05-2014 CrysAlis171 .NET)
(compiled May 22 2014,16:03:01)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_reflns_odcompleteness_completeness 99.85
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     74.33
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H) groups
2.a Aromatic/amide H refined with riding coordinates:
 N2(H1), C3(H2), C4(H3)
;
_olex2_date_sample_data_collection 2018-02-14
_olex2_submission_special_instructions 'No special instructions were received'