Experimental tests for quality validation of computationally predicted crystal structures – a case of a conformationally flexible procyanidin A-2 dihydrate
Dudek, Marta K.; Bujacz, Grzegorz; Potrzebowski, Marek J.; CrystEngComm  (2017) –; doi:10.1039/C7CE00618G

data_7228269
_publ_section_title
;
 Experimental tests for quality validation of computationally predicted
 crystal structures -- a case of a conformationally flexible procyanidin
 A-2 dihydrate
;
_journal_name_full               CrystEngComm
_journal_paper_doi               10.1039/C7CE00618G
_journal_year                    2017
_chemical_absolute_configuration ad
_chemical_compound_source        yes
_chemical_formula_moiety         'C30 H24 O12, 2(H2 O)'
_chemical_formula_sum            'C30 H28 O14'
_chemical_formula_weight         612.52
_chemical_name_common            'Procyanidyn A2'
_chemical_name_systematic
(2R,3R,8S,14R,15R)-2,8-bis(3,4-dihydroxyphenyl)-2,3,4,14-tetrahydro-8,14-methanobenzo[7,8][1,3]dioxocino[4,5-h]chromene-3,5,11,13,15-pentaol
_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
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_update_record
;
2016-11-25 deposited with the CCDC.
2017-05-10 downloaded from the CCDC.
;
_cell_angle_alpha                90.0
_cell_angle_beta                 90.0
_cell_angle_gamma                90.0
_cell_formula_units_Z            4
_cell_length_a                   7.17009(12)
_cell_length_b                   13.9391(2)
_cell_length_c                   25.7472(4)
_cell_measurement_reflns_used    12264
_cell_measurement_temperature    100.0(1)
_cell_measurement_theta_max      75.2820
_cell_measurement_theta_min      3.3840
_cell_volume                     2573.29(7)
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL (Sheldrick, 2008)'
_computing_structure_solution    'SHELXS-97 (Sheldrick, 1990)'
_diffrn_ambient_temperature      100.0(1)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 4.1685
_diffrn_detector_type            TitanS2
_diffrn_measured_fraction_theta_full 0.9996
_diffrn_measured_fraction_theta_max 0.9836
_diffrn_measurement_details
;
  1 omega  -49.00   11.00   1.0000    8.0000
omega____ theta____ kappa____ phi______ frames
    -      -43.7274   37.0000 -150.0000 60

  2 omega   31.00   91.00   1.0000    8.0000
omega____ theta____ kappa____ phi______ frames
    -       43.7274 -125.0000  -30.0000 60

  3 omega   30.00   95.00   1.0000    8.0000
omega____ theta____ kappa____ phi______ frames
    -       43.7274 -125.0000   90.0000 65

  4 omega   28.00  108.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090  -94.0000  120.0000 80

  5 omega   94.00  119.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090 -125.0000    0.0000 25

  6 omega   42.00  136.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090  -77.0000 -120.0000 94

  7 omega   75.00  105.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090  -94.0000 -180.0000 30

  8 omega   34.00   88.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090  -30.0000 -180.0000 54

  9 omega   36.00   89.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090  -30.0000 -120.0000 53

 10 omega   45.00   92.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090  -45.0000    0.0000 47

 11 omega   67.00  178.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090   15.0000   90.0000 111

 12 omega  107.00  155.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090  125.0000  -30.0000 48

 13 omega   83.00  175.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090   45.0000  150.0000 92

 14 omega   37.00   97.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090  -45.0000  120.0000 60

 15 omega   32.00  102.00   1.0000   24.0000
omega____ theta____ kappa____ phi______ frames
    -      106.7090  -94.0000   30.0000 70

 16 omega -123.00   21.00   1.0000    8.0000
omega____ theta____ kappa____ phi______ frames
    -      -43.7274    0.0000 -180.0000 144

;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at zero, TitanS2'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_UB_11      -0.1763067000
_diffrn_orient_matrix_UB_12      0.0623671000
_diffrn_orient_matrix_UB_13      -0.0054096000
_diffrn_orient_matrix_UB_21      0.1025659000
_diffrn_orient_matrix_UB_22      0.0652307000
_diffrn_orient_matrix_UB_23      -0.0389642000
_diffrn_orient_matrix_UB_31      -0.0674200000
_diffrn_orient_matrix_UB_32      -0.0637937000
_diffrn_orient_matrix_UB_33      -0.0450998000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0297
_diffrn_reflns_av_sigmaI/netI    0.0397
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -17
_diffrn_reflns_limit_l_max       31
_diffrn_reflns_limit_l_min       -31
_diffrn_reflns_number            19455
_diffrn_reflns_theta_full        66.9682
_diffrn_reflns_theta_max         75.5736
_diffrn_reflns_theta_min         3.1704
_diffrn_source                   'sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.084
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.77593
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro, Agilent Technologies,
Version 1.171.37.35g (release 09-12-2014 CrysAlis171 .NET)
(compiled Dec  9 2014,15:38:47)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colorless
_exptl_crystal_density_diffrn    1.581
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       nidle
_exptl_crystal_F_000             1280
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: ethanol/water'
_exptl_crystal_size_max          0.25
_exptl_crystal_size_mid          0.05
_exptl_crystal_size_min          0.04
_refine_diff_density_max         0.214
_refine_diff_density_min         -0.185
_refine_diff_density_rms         0.041
_refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881'
_refine_ls_abs_structure_Flack   -0.02(13)
_refine_ls_extinction_coef       0.00144(17)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     SHELXL
_refine_ls_goodness_of_fit_ref   1.041
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     413
_refine_ls_number_reflns         5244
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.041
_refine_ls_R_factor_all          0.0358
_refine_ls_R_factor_gt           0.0343
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0543P)^2^+0.4992P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0914
_refine_ls_wR_factor_ref         0.0931
_reflns_number_gt                5038
_reflns_number_total             5244
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            c7ce00618g2.cif
_cod_data_source_block           procjanidyna_A2
_cod_original_cell_volume        2573.30(7)
_cod_database_code               7228269
_cell_oxdiff_length_a            7.1713(2)
_cell_oxdiff_length_b            13.9394(3)
_cell_oxdiff_length_c            25.7424(5)
_cell_oxdiff_angle_alpha         89.9832(17)
_cell_oxdiff_angle_beta          89.9910(19)
_cell_oxdiff_angle_gamma         89.989(2)
_cell_oxdiff_volume              2573.30(10)
_cell_oxdiff_measurement_reflns_used 12264
_reflns_odcompleteness_completeness 99.96
_reflns_odcompleteness_theta     66.97
_reflns_odcompleteness_iscentric 1
_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, All O(H,H) groups
2.a Free rotating group:
 O12(H12A,H12B), O10(H10A,H10B)
2.b Ternary CH refined with riding coordinates:
 C3(H3A), C4(H4A), C2'(H2'A), C3'(H3'A)
2.c Secondary CH2 refined with riding coordinates:
 C4'(H4'A,H4'B)
2.d Aromatic/amide H refined with riding coordinates:
 C6(H6A), C8(H8), C12(H12), C15(H15), C16(H16), C6'(H6'A), C12'(H12'),
 C15'(H15'), C16'(H16')
2.e Idealised tetrahedral OH refined as rotating group:
 O2(H2), O3(H3), O4(H4), O5(H5), O6(H6), O2'(H2'), O3'(H3'), O5'(H5'), O6'(H6')
;
_olex2_submission_special_instructions 'No special instructions were received'