A Double-Decker Cage for Allosteric Encapsulation of ATP
Badjic, Jovica D.; Xie, Han; Finnegan, Tyler J.; Liyana Gunawardana, Vageesha W.; Moore, Curtis; Xie, William; Chemical Communications  (2022) –; doi:10.1039/D2CC00927G

data_7129954
_publ_section_title
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 A Double-Decker Cage for Allosteric Encapsulation of ATP
;
_journal_name_full               'Chemical Communications'
_journal_paper_doi               10.1039/D2CC00927G
_journal_year                    2022
_chemical_formula_moiety         'C90 H102 N12 O6, 6(C3 H7 N O)'
_chemical_formula_sum            'C108 H144 N18 O12'
_chemical_formula_weight         1886.40
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_atom_sites_solution_secondary   difmap
_audit_creation_date             2022-02-09
_audit_creation_method
;
Olex2 1.5-alpha
(compiled 2021.12.21 svn.raa29eb21 for OlexSys, GUI svn.r6440)
;
_audit_update_record
;
2022-02-14 deposited with the CCDC.	2022-04-04 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 116.128(6)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   26.854(3)
_cell_length_b                   16.764(3)
_cell_length_c                   27.767(4)
_cell_measurement_reflns_used    9382
_cell_measurement_temperature    100.0
_cell_measurement_theta_max      21.762
_cell_measurement_theta_min      2.434
_cell_volume                     11223(3)
_computing_cell_refinement       'SAINT V8.40B (Bruker, 2021)'
_computing_data_collection       'APEX3 v2017.3-0 (Bruker, 2017)'
_computing_data_reduction        'SAINT V8.40B (Bruker, 2021)'
_computing_molecular_graphics    'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL  (Sheldrick, 2008)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100.0
_diffrn_detector                 'Bruker APEX-II CCD'
_diffrn_detector_area_resol_mean 7.9
_diffrn_detector_type            'CCD Area Detector'
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.999
_diffrn_measurement_device       'Kappa Four-Circle Diffractometer'
_diffrn_measurement_device_type  'Nonius Kappa APEX II'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_radiation_xray_symbol    K-L~3~
_diffrn_reflns_av_R_equivalents  0.0514
_diffrn_reflns_av_unetI/netI     0.0230
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       32
_diffrn_reflns_limit_h_min       -32
_diffrn_reflns_limit_k_max       20
_diffrn_reflns_limit_k_min       -20
_diffrn_reflns_limit_l_max       33
_diffrn_reflns_limit_l_min       -33
_diffrn_reflns_number            180560
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         25.365
_diffrn_reflns_theta_min         1.480
_diffrn_source                   'sealed tube'
_diffrn_source_current           30.0
_diffrn_source_power             1.5
_diffrn_source_type              fine-focus
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.074
_exptl_absorpt_correction_T_max  0.0439
_exptl_absorpt_correction_T_min  0.0246
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.0555 before and 0.0515 after correction.
The Ratio of minimum to maximum transmission is 0.5604.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            Colorless
_exptl_crystal_colour_primary    Colorless
_exptl_crystal_density_diffrn    1.117
_exptl_crystal_description       Block
_exptl_crystal_F_000             4056
_exptl_crystal_size_max          0.418
_exptl_crystal_size_mid          0.256
_exptl_crystal_size_min          0.224
_refine_diff_density_max         0.539
_refine_diff_density_min         -0.631
_refine_diff_density_rms         0.053
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.024
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     704
_refine_ls_number_reflns         10288
_refine_ls_number_restraints     147
_refine_ls_restrained_S_all      1.038
_refine_ls_R_factor_all          0.0974
_refine_ls_R_factor_gt           0.0737
_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^)+(0.1218P)^2^+16.0729P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2096
_refine_ls_wR_factor_ref         0.2302
_reflns_Friedel_coverage         0.000
_reflns_number_gt                7345
_reflns_number_total             10288
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2cc00927g2.cif
_cod_data_source_block           Badjic_HX20190814
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_diffrn_radiation_probe' value 'X-ray' was changed to
'x-ray' in accordance with the
/home/data/users/saulius/crontab/automatic-downloads/rss-feeds/RSC/lib/dictionaries/cif_core.dic
dictionary named 'cif_core.dic' version 2.4.2 last updated on
2011-04-26.

Automatic conversion script
Id: cif_fix_values 7556 2019-12-06 15:28:31Z antanas 
;
_cod_original_cell_volume        11222(3)
_cod_database_code               7129954
_shelx_shelxl_version_number     2019/1
_shelx_estimated_absorpt_t_max   0.984
_shelx_estimated_absorpt_t_min   0.970
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, H6 of N6, H2 of N2, H4 of N4, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, H5 of N5, H1 of N1, H3 of N3
2. Restrained distances
 N5-H5 = N3-H3 = N1-H1
 0.95 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(C11S) = Uanis(C11B)
Uanis(C12S) = Uanis(C12B)
Uanis(C10B) = Uanis(C10S)
Uanis(O4B) = Uanis(O4S)
Uanis(N4B) = Uanis(N4S)
4. Rigid body (RIGU) restrains
 O2S, N2S, C4S, C5S, C6S
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 O3S, C9S
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 O4S, N4S, C10S, C11S, C12S, O4B, N4B, C10B, C11B, C12B
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 O3S, N3S, C7S, C8S, C9S
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
5. Same fragment restrains
{O3S, N3S, C7S, C9S, C8S} sigma for 1-2: 0.02, 1-3: 0.02
{O4B, N4B, C10B, C11B, C12B} sigma for 1-2: 0.02, 1-3: 0.02
{O4S, N4S, C10S, C11S, C12S} sigma for 1-2: 0.02, 1-3: 0.02
as in
{O1S, N1S, C1S, C2S, C3S}
6. Others
 Fixed Sof: O2S(0.5) N2S(0.5) C4S(0.5) H4S(0.5) C5S(0.5) H5SA(0.5) H5SB(0.5)
 H5SC(0.5) C6S(0.5) H6SA(0.5) H6SB(0.5) H6SC(0.5) O3S(0.5) N3S(0.5) C7S(0.5)
 H7S(0.5) C9S(0.5) H9SA(0.5) H9SB(0.5) H9SC(0.5) C8S(0.5) H8SA(0.5) H8SB(0.5)
 H8SC(0.5) O4S(0.5) N4S(0.5) C10S(0.5) H10S(0.5) C11S(0.5) H11A(0.5) H11B(0.5)
 H11C(0.5) C12S(0.5) H12A(0.5) H12B(0.5) H12C(0.5) O4B(0.5) N4B(0.5) C10B(0.5)
 H10B(0.5) C11B(0.5) H11D(0.5) H11E(0.5) H11F(0.5) C12B(0.5) H12D(0.5)
 H12E(0.5) H12F(0.5)
7.a Secondary CH2 refined with riding coordinates:
 C7(H7A,H7B), C8(H8A,H8B), C16(H16A,H16B), C18(H18A,H18B), C20(H20A,H20B),
 C21(H21A,H21B), C29(H29A,H29B), C31(H31A,H31B), C33(H33A,H33B), C34(H34A,H34B),
  C42(H42A,H42B), C44(H44A,H44B)
7.b Aromatic/amide H refined with riding coordinates:
 N2(H2), N4(H4), N6(H6), C10(H10), C12(H12), C13(H13), C14(H14), C23(H23),
 C25(H25), C26(H26), C27(H27), C36(H36), C38(H38), C39(H39), C40(H40), C1S(H1S),
  C4S(H4S), C7S(H7S), C10S(H10S), C10B(H10B)
7.c Idealised Me refined as rotating group:
 C19(H19A,H19B,H19C), C32(H32A,H32B,H32C), C45(H45A,H45B,H45C), C2S(H2SA,H2SB,
 H2SC), C3S(H3SA,H3SB,H3SC), C5S(H5SA,H5SB,H5SC), C6S(H6SA,H6SB,H6SC), C9S(H9SA,
 H9SB,H9SC), C8S(H8SA,H8SB,H8SC), C11S(H11A,H11B,H11C), C12S(H12A,H12B,H12C),
 C11B(H11D,H11E,H11F), C12B(H12D,H12E,H12F)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 360 electrons were 
found in a volume of 1344\%A^3^ in 2 voids per unit cell. 
This is consistent with the presence of 0.5[C3H7NO], 
0.5[C4H10O] per Asymmetric Unit which accounts for 328 
electrons per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              98240
_shelx_hkl_checksum              32909
_shelx_fab_checksum              2591
_olex2_submission_special_instructions 'No special instructions were received'