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_2021096
_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
'5Na +, 3C13 H18 N5 O9 P2 -, C13 H17 N5 O9 P2 2-, 24H2 O'
_chemical_formula_moiety
'5(Na +), 3(C13 H18 N5 O9 P2 -), (C13 H17 N5 O9 P2 2-), 24(H2 O)'
_chemical_formula_sum            'C52 H119 N20 Na5 O60 P8'
_chemical_formula_weight         2347.38
_chemical_name_systematic
;
Pentasodium tetrakis(2':3'-isopropylideneadenosine 5'-hypodiphosphate)
tetracosahydrate
;
_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                 120.90(3)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   37.656(8)
_cell_length_b                   7.031(2)
_cell_length_c                   21.959(4)
_cell_measurement_reflns_used    1935
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      63.36
_cell_measurement_theta_min      2.34
_cell_volume                     4989(3)
_computing_cell_refinement
;
CrysAlis RED (Oxford Diffraction, 2010)
;
_computing_data_collection
;
CrysAlis CCD (Oxford Diffraction, 2010)
;
_computing_data_reduction
;
CrysAlis RED (Oxford Diffraction, 2010)
;
_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 8.1956
_diffrn_measured_fraction_theta_full 0.967
_diffrn_measured_fraction_theta_max 0.967
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type
;
Oxford Diffraction Xcalibur PX kappa-geometry diffractometer
with an Onyx CCD camera
;
_diffrn_measurement_method       'omega scans'
_diffrn_radiation_source         'Enhance (Cu) X-ray Source'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.5418
_diffrn_reflns_av_R_equivalents  0.0679
_diffrn_reflns_limit_h_max       31
_diffrn_reflns_limit_h_min       -43
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -8
_diffrn_reflns_limit_l_max       25
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            8179
_diffrn_reflns_theta_full        63.453
_diffrn_reflns_theta_max         63.453
_diffrn_reflns_theta_min         2.345
_exptl_absorpt_coefficient_mu    2.533
_exptl_absorpt_correction_T_max  0.954
_exptl_absorpt_correction_T_min  0.591
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
[CrysAlis RED (Oxford Diffraction, 2010), based on expressions derived
by Clark & Reid (1995)]
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.563
_exptl_crystal_description       needle
_exptl_crystal_F_000             2452
_exptl_crystal_size_max          0.49
_exptl_crystal_size_mid          0.05
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.576
_refine_diff_density_min         -0.415
_refine_ls_abs_structure_details
;
Flack <i>x</i> determined using 532 quotients [(I+)-(I-)]/[(I+)+(I-)]
(Parsons <i>et al.</i>,  2013)
;
_refine_ls_abs_structure_Flack   -0.01(6)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.001
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     770
_refine_ls_number_reflns         5690
_refine_ls_number_restraints     155
_refine_ls_restrained_S_all      1.004
_refine_ls_R_factor_all          0.1409
_refine_ls_R_factor_gt           0.0816
_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^)+(0.0840P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1821
_refine_ls_wR_factor_ref         0.1993
_reflns_number_gt                2724
_reflns_number_total             5690
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            jx3010sup1.cif
_cod_data_source_block           1_otreb50a
_cod_original_cell_volume        4989(2)
_cod_database_code               2021096
_shelx_estimated_absorpt_t_min   0.370
_shelx_estimated_absorpt_t_max   0.951
_shelx_hkl_checksum              95935
_shelx_res_checksum              18885
_cod_database_fobs_code 2021096