Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the adenine‒hypodiphosphate interaction mode in hypodiphosphate nucleotides and adenine salts
Otreba, Marta; Budzikur, Daria; Górecki, Łukasz; Ślepokura, Katarzyna A.; Acta Crystallographica Section C 74 (2018) 571–583; doi:10.1107/S2053229618005089

data_2021097
_publ_section_title
;
 Adenosine hypodiphosphate ester, an analogue of ADP: analysis of the
 adenine--hypodiphosphate interaction mode in hypodiphosphate nucleotides
 and adenine salts
;
_journal_coeditor_code           JX3010
_journal_issue                   5
_journal_name_full               'Acta Crystallographica Section C'
_journal_page_first              571
_journal_page_last               583
_journal_paper_doi               10.1107/S2053229618005089
_journal_volume                  74
_journal_year                    2018
_chemical_formula_iupac
'Na +, C13 H20 N5 O9 P2 +, 2C13 H18 N5 O9 P2 -, C13 H19 N5 O9 P2, 15H2 O'
_chemical_formula_moiety
;
Na +, (C13 H20 N5 O9 P2 +), 2(C13 H18 N5 O9 P2 -), (C13 H19 N5 O9 P2), 15(H2 O)
;
_chemical_formula_sum            'C52 H105 N20 Na O51 P8'
_chemical_formula_weight         2097.30
_chemical_name_systematic
;
Sodium tetrakis(2':3'-isopropylideneadenosine 5'-hypodiphosphate)
pentadecahydrate
;
_space_group_crystal_system      monoclinic
_space_group_IT_number           5
_space_group_name_Hall           'C 2y'
_space_group_name_H-M_alt        'C 1 2 1'
_symmetry_space_group_name_Hall  'C 2y'
_symmetry_space_group_name_H-M   'C 1 2 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_method           SHELXL-2014/7
_cell_angle_alpha                90
_cell_angle_beta                 115.18(3)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   39.474(9)
_cell_length_b                   6.964(2)
_cell_length_c                   18.656(5)
_cell_measurement_reflns_used    5230
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      73.18
_cell_measurement_theta_min      4.29
_cell_volume                     4641(2)
_computing_cell_refinement
;
CrysAlis PRO (Rigaku OD, 2015)
;
_computing_data_collection
;
CrysAlis PRO (Rigaku OD, 2015)
;
_computing_data_reduction
;
CrysAlis PRO (Rigaku OD, 2015)
;
_computing_molecular_graphics
;
DIAMOND (Brandenburg, 2014)
;
_computing_publication_material
;
PLATON (Spek, 2009)
;
_computing_structure_refinement
;
SHELXL2014 (Sheldrick, 2015b)
;
_computing_structure_solution
;
SHELXT2014 (Sheldrick, 2015a)
;
_diffrn_ambient_temperature      100(2)
_diffrn_detector_area_resol_mean 10.3568
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type
;
Agilent Technologies SuperNova, Dual, Cu at zero kappa-geometry
diffractometer with an Atlas CCD camera
;
_diffrn_measurement_method       'omega scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.5418
_diffrn_reflns_av_R_equivalents  0.1561
_diffrn_reflns_limit_h_max       47
_diffrn_reflns_limit_h_min       -47
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -8
_diffrn_reflns_limit_l_max       22
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            23938
_diffrn_reflns_theta_full        67.680
_diffrn_reflns_theta_max         67.999
_diffrn_reflns_theta_min         4.301
_exptl_absorpt_coefficient_mu    2.408
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.228
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
(CrysAlis PRO; Rigaku OD, 2015)
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.501
_exptl_crystal_description       plate
_exptl_crystal_F_000             2192
_exptl_crystal_size_max          0.34
_exptl_crystal_size_mid          0.04
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.823
_refine_diff_density_min         -0.659
_refine_ls_abs_structure_details
;
Flack <i>x</i> determined using 1500 quotients [(I+)-(I-)]/[(I+)+(I-)]
(Parsons <i>et al.</i>,  2013)
;
_refine_ls_abs_structure_Flack   -0.03(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.082
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     682
_refine_ls_number_reflns         8375
_refine_ls_number_restraints     79
_refine_ls_restrained_S_all      1.083
_refine_ls_R_factor_all          0.1339
_refine_ls_R_factor_gt           0.1022
_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^)+(0.1799P)^2^+1.5534P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2710
_refine_ls_wR_factor_ref         0.3093
_reflns_number_gt                5726
_reflns_number_total             8375
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            jx3010sup1.cif
_cod_data_source_block           2_exp60
_cod_database_code               2021097
_shelx_estimated_absorpt_t_min   0.495
_shelx_estimated_absorpt_t_max   0.953
_shelx_hkl_checksum              71450
_shelx_res_checksum              202
_cod_database_fobs_code 2021097