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_2108758
_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_absolute_configuration ad
_chemical_formula_iupac          'C5 H12 O5'
_chemical_formula_moiety         'C5 H12 O5'
_chemical_formula_sum            'C5 H12 O5'
_chemical_formula_weight         152.15
_chemical_name_common            Xylitol
_chemical_name_systematic
;
(2<i>R</i>,3<i>R</i>,4<i>S</i>)-Pentane-1,2,3,4,5-pentol
;
_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   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2019-03-15
_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                   8.2707(2)
_cell_length_b                   8.9022(2)
_cell_length_c                   8.9217(2)
_cell_measurement_reflns_used    8709
_cell_measurement_temperature    122.98(10)
_cell_measurement_theta_max      76.8430
_cell_measurement_theta_min      4.9330
_cell_volume                     656.88(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      122.98(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.4391
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_details
;
  1 omega  -92.00   -2.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      -41.2813  125.0000   60.0000 90

  2 omega -129.00   47.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      -41.2813    0.0000   60.0000 176

  3 omega  -66.00   33.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      -41.2813   37.0000 -120.0000 99

  4 omega    9.00  117.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -       41.2813   77.0000  150.0000 108

  5 omega    9.00  117.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -       41.2813   77.0000 -120.0000 108

  6 omega   11.00  114.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -       41.2813   65.0000  -70.9723 103

  7 omega   23.00   97.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -       41.2813 -125.0000  -30.0000 74

  8 omega    9.00  117.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -       41.2813   77.0000  -30.0000 108

  9 omega   23.00   97.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -       41.2813 -125.0000   60.0000 74

 10 omega    9.00  117.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -       41.2813   77.0000   60.0000 108

 11 omega   17.00  116.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -       41.2813   37.0000 -120.0000 99

 12 omega   79.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000 -150.0000 99

 13 omega   36.00  113.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000 -111.0000 -120.0000 77

 14 omega   82.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   65.0000   37.8339 96

 15 omega   36.00  145.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000  -77.0000  -90.0000 109

 16 omega   82.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   64.0000  151.6815 96

 17 omega   79.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000  -30.0000 99

 18 omega   83.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   61.0000 -150.0000 95

 19 omega   79.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000   60.0000 99

 20 omega   79.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000 -120.0000 99

 21 omega   83.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   61.0000 -180.0000 95

 22 omega   36.00  113.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000 -111.0000    0.0000 77

 23 omega   83.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   61.0000  120.0000 95

 24 omega   79.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000  150.0000 99

 25 omega   79.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000  120.0000 99

 26 omega   83.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   61.0000   90.0000 95

 27 omega   82.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   68.0000   51.5464 96

 28 omega   81.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   71.0000  100.7861 97

 29 omega  125.00  169.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   61.0000  -60.0000 44

 30 omega   79.00  108.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000 -111.0000   60.0000 29

 31 omega   86.00  113.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   61.0000  -60.0000 27

 32 omega   84.00  111.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   61.0000  -30.0000 27

 33 omega   83.00  127.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   61.0000  -90.0000 44

 34 omega  110.00  177.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000  -90.0000 67

 35 omega  138.00  171.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   56.0000    9.4110 33

 36 omega   83.00  136.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   61.0000   30.0000 53

 37 omega   37.00  108.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000 -111.0000  -90.0000 71

 38 omega   51.00  107.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000 -111.0000 -150.0000 56

 39 omega   84.00  115.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   61.0000 -120.0000 31

 40 omega   35.00  110.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000  -94.0000   90.0000 75

 41 omega   79.00  105.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000  -90.0000 26

 42 omega   86.00  114.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   45.0000  120.0000 28

 43 omega   79.00  106.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000 -180.0000 27

 44 omega  114.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000 -180.0000 64

 45 omega   80.00  107.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000  -60.0000 27

 46 omega  153.00  178.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000  -60.0000 25

 47 omega   63.00   91.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000 -111.0000  150.0000 28

 48 omega   86.00  115.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   45.0000 -120.0000 29

 49 omega   87.00  118.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   45.0000    0.0000 31

 50 omega   79.00  106.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   77.0000    0.0000 27

 51 omega   88.00  120.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   45.0000  150.0000 32

 52 omega   84.00  132.00   1.0000    1.0000
omega____ theta____ kappa____ phi______ frames
    -      112.0000   56.0000    9.4110 48
;
_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      -0.1090536000
_diffrn_orient_matrix_UB_12      0.0558810000
_diffrn_orient_matrix_UB_13      0.1284291000
_diffrn_orient_matrix_UB_21      0.1509827000
_diffrn_orient_matrix_UB_22      0.0352168000
_diffrn_orient_matrix_UB_23      0.0949318000
_diffrn_orient_matrix_UB_31      0.0048767000
_diffrn_orient_matrix_UB_32      0.1598542000
_diffrn_orient_matrix_UB_33      -0.0657842000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0464
_diffrn_reflns_av_unetI/netI     0.0152
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       11
_diffrn_reflns_limit_l_min       -11
_diffrn_reflns_number            14853
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.996
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         76.763
_diffrn_reflns_theta_min         7.027
_diffrn_source                   'sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.204
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.38260
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
(CrysAlis PRO; Agilent, 2014)
;
_exptl_crystal_density_diffrn    1.538
_exptl_crystal_description
;
;
_exptl_crystal_F_000             328
_exptl_crystal_size_max          0.35
_exptl_crystal_size_mid          0.22
_exptl_crystal_size_min          0.18
_refine_diff_density_max         0.317
_refine_diff_density_min         -0.208
_refine_diff_density_rms         0.050
_refine_ls_abs_structure_details
;
Flack <i>x</i> determined using 550 quotients [(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013)
;
_refine_ls_abs_structure_Flack   0.03(7)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.092
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     99
_refine_ls_number_reflns         1383
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.092
_refine_ls_R_factor_all          0.0283
_refine_ls_R_factor_gt           0.0281
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0541P)^2^+0.0779P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0763
_refine_ls_wR_factor_ref         0.0768
_reflns_Friedel_coverage         0.672
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.995
_reflns_number_gt                1370
_reflns_number_total             1383
_reflns_threshold_expression     'I > 2\s(I)'
_publcif_datablock.id            {958c04c6-b933-418f-832c-c0d50359a9bf}
_cod_data_source_file            px5028sup1.cif
_cod_data_source_block           2Cu
_cod_database_code               2108758
_cod_database_fobs_code          2108758
_shelx_shelxl_version_number     2016/4
_chemical_oxdiff_formula         C5H12O5
_chemical_oxdiff_usercomment     colourless
_shelx_estimated_absorpt_t_max   0.812
_shelx_estimated_absorpt_t_min   0.678
_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.
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_reflns_odcompleteness_completeness 99.88
_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 C(H,H) groups
 At 1.5 times of:
  All O(H) groups
2.a Ternary CH refined with riding coordinates:
 C3(H3), C4(H4), C2(H2)
2.b Secondary CH2 refined with riding coordinates:
 C1(H1A,H1B), C5(H5A,H5B)
2.c Idealised tetrahedral OH refined as rotating group:
 O2(H12), O3(H13), O5(H15), O1(H11)
;
_olex2_date_sample_data_collection 2019-03-15
_olex2_submission_special_instructions 'No special instructions were received'