Thermal stability and conformation of antiparallel duplexes formed by P-stereodefined phosphorothioate DNA/LNA chimeric oligomers with DNA and RNA matrices.
Jastrzębska, Katarzyna; Maciaszek, Anna; Dolot, Rafał; Bujacz, Grzegorz; Guga, Piotr; Organic & biomolecular chemistry 13 (2015) 10032–10040; doi:10.1039/c5ob01474c

data_7154642
_publ_section_title
;
 Thermal stability and conformation of antiparallel duplexes formed by
 P-stereodefined phosphorothioate DNA/LNA chimeric oligomers with DNA and
 RNA matrices.
;
_journal_issue                   39
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              10032
_journal_page_last               10040
_journal_paper_doi               10.1039/c5ob01474c
_journal_volume                  13
_journal_year                    2015
_chemical_absolute_configuration ad
_chemical_compound_source        synthetic
_chemical_formula_moiety         'C18 H25 N2 O7 P S2'
_chemical_formula_sum            'C18 H25 N2 O7 P S2'
_chemical_formula_weight         476.49
_chemical_melting_point          403
_chemical_name_common
thymidine-LNA-3'-O-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane)
_chemical_name_systematic
thymin-1-yl-2'-O,4'-C-methylene-\b-D-ribofuranosyl-3'-O-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane)
_chemical_properties_physical    Moisture-sensitive
_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'
_symmetry_cell_setting           orthorhombic
_symmetry_Int_Tables_number      19
_symmetry_space_group_name_Hall  'P 2ac 2ab'
_symmetry_space_group_name_H-M   'P 21 21 21'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_date             2015-03-31
_audit_creation_method
;
Olex2 1.2
(compiled 2015.01.26 svn.r3150 for OlexSys, GUI svn.r4998)
;
_audit_update_record
;
2015-04-27 deposited with the CCDC.
2015-08-13 downloaded from the CCDC.
;
_cell_angle_alpha                90.00
_cell_angle_beta                 90.00
_cell_angle_gamma                90.00
_cell_formula_units_Z            4
_cell_length_a                   6.37110(10)
_cell_length_b                   12.1422(3)
_cell_length_c                   27.2294(7)
_cell_measurement_temperature    100(2)
_cell_volume                     2106.44(8)
_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_pressure         101.30
_diffrn_ambient_temperature      100.15
_diffrn_measured_fraction_theta_full 0.979
_diffrn_measured_fraction_theta_max 0.980
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0344
_diffrn_reflns_av_unetI/netI     0.0491
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -7
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       28
_diffrn_reflns_limit_l_min       -34
_diffrn_reflns_number            7619
_diffrn_reflns_theta_full        74.97
_diffrn_reflns_theta_max         74.97
_diffrn_reflns_theta_min         3.99
_diffrn_source                   'fine-focus sealed tube'
_diffrn_source_type              'SuperNova Agilent Technologies'
_exptl_absorpt_coefficient_mu    3.405
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.502
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       prism
_exptl_crystal_F_000             1000
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: acetonitrile'
_exptl_crystal_size_max          0.10
_exptl_crystal_size_mid          0.05
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.268
_refine_diff_density_min         -0.323
_refine_diff_density_rms         0.062
_refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881'
_refine_ls_abs_structure_Flack   0.010(15)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.032
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     273
_refine_ls_number_reflns         4177
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.032
_refine_ls_R_factor_all          0.0360
_refine_ls_R_factor_gt           0.0310
_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^)+(0.0387P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0726
_refine_ls_wR_factor_ref         0.0750
_reflns_number_gt                3851
_reflns_number_total             4177
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            c5ob01474c2.cif
_cod_data_source_block           gugaA
_cod_depositor_comments          'Adding full bibliography for 7154642.cif.'
_cod_database_code               7154642
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2.a Ternary CH refined with riding coordinates:
 C1'(H1'), C2'(H2'), C3'(H3')
2.b Secondary CH2 refined with riding coordinates:
 C4"(H4"A,H4"B), C5'(H5'A,H5'B), C8(H8A,H8B), C10(H10A,H10B), C11(H11A,H11B),
 C12(H12A,H12B), C13(H13A,H13B), C14(H14A,H14B)
2.c Aromatic/amide H refined with riding coordinates:
 N3(H3), C6(H6)
2.d Idealised Me refined as rotating group:
 C7(H7A,H7B,H7C)
2.e Idealised tetrahedral OH refined as rotating group:
 O5'(H5')
;