Discovery of a cyclic 6 + 6 hexamer of d-biotin and formaldehyde
Lisbjerg, Micke; Jessen, Bo M.; Rasmussen, Brian; Nielsen, Bjarne E.; Madsen, Anders Ø.; Pittelkow, Michael; Chemical Science 5 (2014) 2647–; doi:10.1039/c4sc00990h

data_1515377
_publ_section_title
;
 Discovery of a cyclic 6 + 6 hexamer of d-biotin and formaldehyde
;
_journal_issue                   7
_journal_name_full               'Chemical Science'
_journal_page_first              2647
_journal_paper_doi               10.1039/c4sc00990h
_journal_volume                  5
_journal_year                    2014
_chemical_absolute_configuration ad
_chemical_formula_moiety         '2(C2 H6 O), C66 H95.62 N12 O18 S6'
_chemical_formula_sum            'C70 H108 N12 O20 S6'
_chemical_formula_weight         1630.04
_chemical_name_systematic        Biotin[6]uril
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_symmetry_space_group_name_Hall  'P 2yb'
_symmetry_space_group_name_H-M   'P 1 21 1'
_atom_sites_solution_hydrogens   mixed
_audit_creation_date             2014-02-24
_audit_creation_method
;
Olex2 1.2
(compiled 2014.02.17 svn.r2891 for OlexSys, GUI svn.r4773)
;
_cell_angle_alpha                90
_cell_angle_beta                 102.322(14)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   12.1810(11)
_cell_length_b                   16.841(4)
_cell_length_c                   20.8050(14)
_cell_measurement_temperature    122
_cell_volume                     4169.6(11)
_computing_cell_refinement       'COLLECT (Nonius, 1999)'
_computing_data_collection       'COLLECT (Nonius, 1999)'
_computing_data_reduction        'EvalCCD (Duisenberg et al., 2003)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2008)'
_computing_structure_solution    'SHELXS-97 (Sheldrick, 1990)'
_diffrn_ambient_temperature      122.15
_diffrn_measured_fraction_theta_full 0.828
_diffrn_measured_fraction_theta_max 0.638
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0678
_diffrn_reflns_av_unetI/netI     0.0533
_diffrn_reflns_Laue_measured_fraction_full 0.828
_diffrn_reflns_Laue_measured_fraction_max 0.638
_diffrn_reflns_limit_h_max       18
_diffrn_reflns_limit_h_min       -17
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -24
_diffrn_reflns_limit_l_max       31
_diffrn_reflns_limit_l_min       -30
_diffrn_reflns_number            30136
_diffrn_reflns_point_group_measured_fraction_full 0.676
_diffrn_reflns_point_group_measured_fraction_max 0.489
_diffrn_reflns_theta_full        25.000
_diffrn_reflns_theta_max         32.978
_diffrn_reflns_theta_min         1.570
_exptl_absorpt_coefficient_mu    0.237
_exptl_absorpt_correction_T_max  0.921
_exptl_absorpt_correction_T_min  0.867
_exptl_absorpt_correction_type   integration
_exptl_absorpt_process_details   'Gaussian integration (Coppens, 1970)'
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.298
_exptl_crystal_description       prism
_exptl_crystal_F_000             1736
_exptl_crystal_size_max          0.98
_exptl_crystal_size_mid          0.61
_exptl_crystal_size_min          0.5
_refine_diff_density_max         0.902
_refine_diff_density_min         -0.654
_refine_diff_density_rms         0.083
_refine_ls_abs_structure_details
;
 Flack x determined using 2908 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons and Flack (2004), Acta Cryst. A60, s61).
;
_refine_ls_abs_structure_Flack   0.05(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.098
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1128
_refine_ls_number_reflns         15339
_refine_ls_number_restraints     121
_refine_ls_restrained_S_all      1.095
_refine_ls_R_factor_all          0.1140
_refine_ls_R_factor_gt           0.0758
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1142P)^2^+5.2586P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2010
_refine_ls_wR_factor_ref         0.2322
_reflns_Friedel_coverage         0.488
_reflns_Friedel_fraction_full    0.512
_reflns_Friedel_fraction_max     0.330
_reflns_number_gt                10292
_reflns_number_total             15339
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c4sc00990h2.cif
_cod_data_source_block           test
_cod_depositor_comments
'Adding full bibliography for 1515377--1515378.cif.'
_cod_original_cell_volume        4169.6(12)
_cod_database_code               1515377
_shelxl_version_number           2013-4
_shelx_estimated_absorpt_t_max   0.891
_shelx_estimated_absorpt_t_min   0.801
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Restrained distances
 C1A-C1B
 1.5 with sigma of 0.02
 C1B-O1A
 1.4 with sigma of 0.02
 C11-C10 \\sim C10-C9
 with sigma of 0.02
3. Rigid bond restraints
 C11, C10
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C1A, C1B
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C162, C161
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 0.9A with sigma of 0.4 and sigma
for terminal atoms of 0.8
Uanis(C361) = Uanis(C261)
Uanis(C263) = Uanis(C163)
5. Rigid body (RIGU) restrains
 C260, S286, C261, C72, C263, C74, C265
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C58, C160, S186, C62, C163, C64, C165, C66
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C243, C244
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(C260)=Sof(H26A)=Sof(H26B)=Sof(S286)=Sof(C261)=Sof(H261)=Sof(C72)=
 Sof(H72A)=Sof(H72B)=Sof(C263)=Sof(H26C)=Sof(H26D)=Sof(C74)=Sof(H74A)=Sof(H74B)=
 Sof(C265)=Sof(H26E)=Sof(H26F)=Sof(C76)=Sof(O28)=Sof(O27)=Sof(H27)=Sof(H58A)=
 Sof(H59A)=1-FVAR(1)
 Sof(C160)=Sof(H16A)=Sof(H16B)=Sof(S186)=Sof(C361)=Sof(H361)=Sof(C62)=Sof(H62)=
 Sof(C163)=Sof(H16C)=Sof(H16D)=Sof(C64)=Sof(H64A)=Sof(H64B)=Sof(C165)=Sof(H16E)=
 Sof(H16F)=Sof(C66)=Sof(O17)=Sof(O18)=Sof(H18)=Sof(H58)=Sof(H59)=FVAR(1)
 Sof(O111)=Sof(O112)=Sof(H112)=Sof(C144)=Sof(C143)=Sof(H14A)=Sof(H14B)=
 Sof(H42C)=Sof(H42D)=1-FVAR(2)
 Sof(O211)=Sof(O212)=Sof(H212)=Sof(C244)=Sof(C243)=Sof(H24A)=Sof(H24B)=
 Sof(H42A)=Sof(H42B)=FVAR(2)
 Sof(C1A)=Sof(H1AA)=Sof(H1AB)=Sof(H1AC)=Sof(O1A)=Sof(H1AD)=Sof(C1B)=Sof(H1BA)=
 Sof(H1BB)=1-FVAR(3)
 Sof(O160)=Sof(H160)=Sof(C161)=Sof(H16G)=Sof(H16H)=Sof(C162)=Sof(H16I)=
 Sof(H16J)=Sof(H16K)=FVAR(3)
7.a Everything fixed:
 H150, H112, H18, H2
7.b Ternary CH refined with riding coordinates:
 C261(H261), C361(H361), C48(H48), C28(H28), C27(H27A), C15(H15), C16(H16),
 C50(H50), C49(H49), C26(H26), C17(H17), C39(H39), C6(H6), C4(H4), C58(H58A),
 C58(H58), C37(H37), C59(H59A), C59(H59), C38(H38), C5(H5)
7.c Secondary CH2 refined with riding coordinates:
 C151(H15B,H15C), C143(H14A,H14B), C243(H24A,H24B), C260(H26A,H26B), C72(H72A,
 H72B), C263(H26C,H26D), C74(H74A,H74B), C265(H26E,H26F), C160(H16A,H16B),
 C163(H16C,H16D), C64(H64A,H64B), C165(H16E,H16F), C161(H16G,H16H), C1(H1A,H1B),
  C29(H29A,H29B), C23(H23A,H23B), C19(H19A,H19B), C12(H12A,H12B), C30(H30A,
 H30B), C18(H18A,H18B), C7(H7A,H7B), C34(H34A,H34B), C20(H20A,H20B), C51(H51A,
 H51B), C31(H31A,H31B), C21(H21A,H21B), C45(H45A,H45B), C53(H53A,H53B),
 C52(H52A,H52B), C25(H25A,H25B), C56(H56A,H56B), C47(H47A,H47B), C14(H14C,H14D),
  C32(H32A,H32B), C9(H9A,H9B), C10(H10A,H10B), C36(H36A,H36B), C8(H8A,H8B),
 C54(H54A,H54B), C3(H3A,H3B), C42(H42C,H42D), C42(H42A,H42B), C41(H41A,H41B),
 C40(H40A,H40B), C1B(H1BA,H1BB)
7.d Me refined with riding coordinates:
 C152(H15D,H15E,H15F)
7.e Idealised Me refined as rotating group:
 C162(H16I,H16J,H16K), C1A(H1AA,H1AB,H1AC)
7.f Idealised tetrahedral OH refined with riding coordinates:
 O212(H212)
7.g Idealised tetrahedral OH refined as rotating group:
 O27(H27), O160(H160), O9(H9), O15(H15A), O6(H6A), O1A(H1AD)
;
_smtbx_masks_special_details
;
The solvent masking procedure as implemented in Olex2 was used to remove the
electronic contribution of solvent molecules from the refinement. Only the
atoms used in the refinement model are reported in the formula here.

Total solvent accessible volume / cell = 354 Ang^3
Total electron count / cell = 72.5
;
_shelx_res_checksum              66481
_olex2_computing_structure_refinement_long 'ShelXL (Sheldrick, 2008)'