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_7129953
_publ_section_title
;
 A Double-Decker Cage for Allosteric Encapsulation of ATP
;
_journal_name_full               'Chemical Communications'
_journal_paper_doi               10.1039/D2CC00927G
_journal_year                    2022
_chemical_absolute_configuration rmad
_chemical_formula_moiety
'C90 H108 N12 O6, 2(C10 H14 N5 O13 P3), 5(H2 O)'
_chemical_formula_sum            'C110 H146 N22 O37 P6'
_chemical_formula_weight         2554.30
_space_group_crystal_system      triclinic
_space_group_IT_number           1
_space_group_name_Hall           'P 1'
_space_group_name_H-M_alt        'P 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_atom_sites_solution_secondary   difmap
_audit_creation_date             2022-02-12
_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                86.620(3)
_cell_angle_beta                 77.207(2)
_cell_angle_gamma                75.033(2)
_cell_formula_units_Z            3
_cell_length_a                   18.8037(15)
_cell_length_b                   22.504(2)
_cell_length_c                   27.891(2)
_cell_measurement_reflns_used    9722
_cell_measurement_temperature    100.0
_cell_measurement_theta_max      26.273
_cell_measurement_theta_min      2.292
_cell_volume                     11118.9(16)
_computing_cell_refinement       'SAINT v8.40B (Bruker, 2021)'
_computing_data_collection       'APEX3 v2021.4-0 (Bruker, 2021)'
_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 Photon III area detector'
_diffrn_detector_area_resol_mean 10.5
_diffrn_detector_type            'CMOS area detector'
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.996
_diffrn_measurement_device       'Kappa Four-Circle Diffractometer'
_diffrn_measurement_device_type  'Bruker D8 Venture'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_monochromator  'Double Bounce Multilayer Mirrors'
_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  0.0705
_diffrn_reflns_av_unetI/netI     0.0528
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.996
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       28
_diffrn_reflns_limit_k_min       -28
_diffrn_reflns_limit_l_max       34
_diffrn_reflns_limit_l_min       -34
_diffrn_reflns_number            708414
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.992
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         26.427
_diffrn_reflns_theta_min         1.873
_diffrn_source                   'Micro Focus Rotating Anode'
_diffrn_source_current           50.0
_diffrn_source_power             2.5
_diffrn_source_type              'Bruker TXS'
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.147
_exptl_absorpt_correction_T_max  0.0274
_exptl_absorpt_correction_T_min  0.0112
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1080 before and 0.0624 after correction.
The Ratio of minimum to maximum transmission is 0.4088.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            Colorless
_exptl_crystal_colour_primary    Colorless
_exptl_crystal_density_diffrn    1.144
_exptl_crystal_description       Block
_exptl_crystal_F_000             4038
_exptl_crystal_size_max          0.176
_exptl_crystal_size_mid          0.134
_exptl_crystal_size_min          0.092
_refine_diff_density_max         1.096
_refine_diff_density_min         -0.386
_refine_diff_density_rms         0.112
_refine_ls_abs_structure_details
;
 Flack x determined using 21366 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.116(18)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   0.995
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     4823
_refine_ls_number_reflns         90765
_refine_ls_number_restraints     4221
_refine_ls_restrained_S_all      1.002
_refine_ls_R_factor_all          0.1155
_refine_ls_R_factor_gt           0.0770
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1442P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1940
_refine_ls_wR_factor_ref         0.2244
_reflns_Friedel_coverage         0.992
_reflns_Friedel_fraction_full    0.996
_reflns_Friedel_fraction_max     0.988
_reflns_number_gt                58072
_reflns_number_total             90765
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2cc00927g2.cif
_cod_data_source_block           Badjic_HX20220107
_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        11118.7(16)
_cod_database_code               7129953
_shelx_shelxl_version_number     2019/1
_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, All N(H) groups,
  All N(H,H) groups, All N(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups, All O(H,H) groups
2. Restrained distances
 O12C-C3C
 1.4 with sigma of 0.005
3. Uiso/Uaniso restraints and constraints
Uanis(O8E) = Uanis(O9F)
Uanis(O10F) = Uanis(O10E)
Uanis(P3E) = Uanis(P3F)
Uanis(O7F) = Uanis(O7E)
Uanis(O8F) = Uanis(O9E)
Uanis(C59") = Uanis(C59B)
Uanis(C54B) = Uanis(C54")
Uanis(C55") = Uanis(C55B)
Uanis(C53") = Uanis(C53B)
4. Rigid body (RIGU) restrains
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5. Others
 Sof(H7"A)=Sof(H7"B)=Sof(H58A)=Sof(C53")=Sof(H53A)=Sof(H53B)=Sof(C54B)=
 Sof(C55B)=Sof(H55B)=Sof(C59B)=Sof(H59B)=1-FVAR(1)
 Sof(H7"C)=Sof(H7"D)=Sof(H58")=Sof(C54")=Sof(C55")=Sof(H55")=Sof(C59")=
 Sof(H59")=Sof(C53B)=Sof(H53C)=Sof(H53D)=FVAR(1)
 Sof(P3F)=Sof(O7F)=Sof(O8F)=Sof(O9F)=Sof(O10F)=Sof(H1FC)=Sof(H1FD)=1-FVAR(2)
 Sof(P3E)=Sof(O7E)=Sof(O8E)=Sof(O9E)=Sof(O10E)=Sof(H1FA)=Sof(H1FB)=FVAR(2)
 Fixed X: H6SA(-0.18533) H6SB(-0.16609) H9SA(-0.03681) H9SB(0.01608) H10G(-
 0.000431) H10H(0.07038) H11G(0.190701) H11H(0.1475)
 Fixed Y: H6SA(0.028101) H6SB(0.0038) H9SA(0.24524) H9SB(0.19235)
 H10G(0.32985) H10H(0.325041) H11G(0.378981) H11H(0.4229)
 Fixed Z: H6SA(-0.41098) H6SB(-0.36905) H9SA(-0.20946) H9SB(-0.221551) H10G(-
 0.202391) H10H(-0.2277) H11G(-0.11916) H11H(-0.14254)
6.a Free rotating group:
 O1S(H1SA,H1SB), O2S(H2SA,H2SB), O3S(H3SA,H3SB), O4S(H4SA,H4SB), O5S(H5SA,
 H5SB), O7S(H7SA,H7SB), O8S(H8SA,H8SB), O12S(H12J,H12K), O13S(H13G,H13H),
 O14S(H14A,H14B), O15S(H15A,H15B)
6.b Ternary CH refined with riding coordinates:
 C2(H2), C3(H3), C4(H4A), C5(H5), C2A(H2A), C3A(H3A), C4A(H4AB), C5A(H5AC),
 C2B(H2B), C3B(H3B), C4B(H4BA), C5B(H5BC), C2C(H2C), C3C(H3C), C4C(H4CA),
 C5C(H5C), C2D(H2D), C3D(H3D), C4D(H4DA), C5D(H5D), C2E(H2E), C3E(H3E),
 C4E(H4EA), C5E(H5E)
6.c Secondary CH2 refined with riding coordinates:
 N1X(H1XC,H1XD), N3X(H3XC,H3XD), N5X(H5XC,H5XD), N7(H7A,H7B), N9(H9A,H9B),
 N11(H11C,H11D), C7X(H7XC,H7XD), C8X(H8XC,H8XD), C16(H16C,H16D), C18(H18C,H18D),
  C20(H20C,H20D), C21(H21C,H21D), C29(H29C,H29D), C31(H31C,H31D), C33(H33C,
 H33D), C34(H34C,H34D), C42(H42C,H42D), C44(H44C,H44D), C52(H52C,H52D),
 C53(H53E,H53F), C61(H61C,H61D), C63(H63C,H63D), C65(H65C,H65D), C66(H66C,H66D),
  C74(H74C,H74D), C76(H76C,H76D), C78(H78C,H78D), C79(H79C,H79D), C87(H87C,
 H87D), C89(H89C,H89D), C1(H1A,H1B), C1G(H1GA,H1GB), N1X'(H1XE,H1XF), N3X'(H3XE,
 H3XF), N5X'(H5XE,H5XF), N7'(H7'A,H7'B), N9'(H9'A,H9'B), N11'(H11E,H11F),
 C7X'(H7XE,H7XF), C8X'(H8XE,H8XF), C16'(H16E,H16F), C18'(H18E,H18F), C20'(H20E,
 H20F), C21'(H21E,H21F), C29'(H29E,H29F), C31'(H31E,H31F), C33'(H33E,H33F),
 C34'(H34E,H34F), C42'(H42E,H42F), C44'(H44E,H44F), C52'(H52E,H52F), C53'(H53G,
 H53H), C61'(H61E,H61F), C63'(H63E,H63F), C65'(H65E,H65F), C66'(H66E,H66F),
 C74'(H74E,H74F), C76'(H76E,H76F), C78'(H78E,H78F), C79'(H79E,H79F), C87'(H87E,
 H87F), C89'(H89E,H89F), C1B(H1BB,H1BC), C1E(H1EA,H1EB), N1X"(H1XA,H1XB),
 N3X"(H3XA,H3XB), N5X"(H5XA,H5XB), N7"(H7"C,H7"D), N7"(H7"A,H7"B), N9"(H9"A,
 H9"B), N11"(H11A,H11B), C7X"(H7XA,H7XB), C8X"(H8XA,H8XB), 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),
 C52"(H52A,H52B), C61"(H61A,H61B), C63"(H63A,H63B), C65"(H65A,H65B), C66"(H66A,
 H66B), C74"(H74A,H74B), C76"(H76A,H76B), C78"(H78A,H78B), C79"(H79A,H79B),
 C87"(H87A,H87B), C89"(H89A,H89B), C53"(H53A,H53B), C53B(H53C,H53D), C1D(H1DA,
 H1DB), C1F(H1FA,H1FB), C1F(H1FC,H1FD)
6.d Aromatic/amide H refined with riding coordinates:
 N2X(H2X), N4X(H4X), N6X(H6X), N8(H8), N10(H10), N12(H12), C1C(H1C), C11(H11),
 C12(H12B), C14(H14), C23(H23), C25(H25), C26(H26), C27(H27), C36(H36),
 C38(H38), C39(H39), C40(H40), C55(H55), C57(H57), C58(H58), C59(H59), C68(H68),
  C70(H70), C71(H71), C72(H72), C81(H81), C83(H83), C84(H84), C85(H85), N4(H4),
 C9(H9), C10(H10A), N4A(H4AA), C9A(H9AA), C10A(H10B), N2X'(H2X'), N4X'(H4X'),
 N6X'(H6X'), N8'(H8'), N10'(H10'), N12'(H12'), C12'(H12C), C13(H13), C13'(H13'),
  C14'(H14'), C23'(H23'), C25'(H25'), C26'(H26'), C27'(H27'), C36'(H36'),
 C38'(H38'), C39'(H39'), C40'(H40'), C55'(H55'), C57'(H57'), C58'(H58'),
 C59'(H59'), C68'(H68'), C70'(H70'), C71'(H71'), C72'(H72'), C81'(H81'),
 C83'(H83'), C84'(H84'), C85'(H85'), N4B(H4B), C9B(H9BA), C10B(H10C), N4C(H4C),
 C9C(H9C), C10C(H10D), N2X"(H2X"), N4X"(H4X"), N6X"(H6X"), N8"(H8"), N10"(H10"),
  N12"(H12"), C10X(H10X), C12"(H12A), C13"(H13"), C14"(H14"), C23"(H23"),
 C25"(H25"), C26"(H26"), C27"(H27"), C36"(H36"), C38"(H38"), C39"(H39"),
 C40"(H40"), C57"(H57"), C58"(H58"), C58"(H58A), C68"(H68"), C70"(H70"),
 C71"(H71"), C72"(H72"), C81"(H81"), C83"(H83"), C84"(H84"), C85"(H85"),
 C55"(H55"), C59"(H59"), C55B(H55B), C59B(H59B), N4D(H4D), C9D(H9D), C10D(H10F),
  N4E(H4E), C9E(H9E), C10E(H10E)
6.e Tetrahedral OH refined with riding coordinates:
 O1(H1)
6.f X=CH2 refined with riding coordinates:
 N5(H5A,H5B), N5A(H5AA,H5AB), N5B(H5BA,H5BB), N5C(H5CA,H5CB), N5D(H5DA,H5DB),
 N5E(H5EA,H5EB)
6.g Idealised Me refined as rotating group:
 C19(H19D,H19E,H19F), C32(H32D,H32E,H32F), C45(H45D,H45E,H45F), C64(H64D,H64E,
 H64F), C77(H77D,H77E,H77F), C90(H90D,H90E,H90F), C19'(H19G,H19H,H19I),
 C32'(H32G,H32H,H32I), C45'(H45G,H45H,H45I), C64'(H64G,H64H,H64I), C77'(H77G,
 H77H,H77I), C90'(H90G,H90H,H90I), C19"(H19A,H19B,H19C), C32"(H32A,H32B,H32C),
 C45"(H45A,H45B,H45C), C64"(H64A,H64B,H64C), C77"(H77A,H77B,H77C), C90"(H90A,
 H90B,H90C)
6.h Idealised tetrahedral OH refined as rotating group:
 O12(H12D), O13(H13A), O1A(H1AA), O12A(H12F), O13A(H13B), O1B(H1BA),
 O12B(H12G), O13B(H13C), O1C(H1CA), O12C(H12H), O13C(H13D), O1D(H1D),
 O12D(H12I), O13D(H13F), O1E(H1E), O12E(H12E), O13E(H13E)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 874 electrons were 
found in a volume of 3049\%A^3^ in 5 voids per unit cell. 
One large void of 2973\%A^3^ was found to contain all of 
the electrons. This is consistent with the presence of 
30[H2O] per complex of interest which accounts for 900 
electrons per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              15357
_shelx_hkl_checksum              24615
_shelx_fab_checksum              14103
_olex2_submission_special_instructions 'No special instructions were received'