Peptide recognition by a synthetic receptor at subnanomolar concentrations
Suating, Paolo; Ewe, Marc B.; Kimberly, Lauren B.; Arman, Hadi D.; Wherritt, Daniel J.; Urbach, Adam R.; Chemical Science 15 (2024) 5133–5142; doi:10.1039/D4SC01122H

data_1571240
_publ_section_title
;
 Peptide recognition by a synthetic receptor at subnanomolar
 concentrations
;
_journal_issue                   14
_journal_name_full               'Chemical Science'
_journal_page_first              5133
_journal_page_last               5142
_journal_paper_doi               10.1039/D4SC01122H
_journal_volume                  15
_journal_year                    2024
_chemical_absolute_configuration ad
_chemical_compound_source        synthetic
_chemical_formula_moiety
'4(C21 H32 N5 O7), 23.2(H2 O), 4(C48 H48 N32 O16), 15(H O), 2(O)'
_chemical_formula_sum            'C276 H381.4 N148 O132.2'
_chemical_formula_weight         7887.87
_chemical_name_common            'LYGGG Q8 complex'
_chemical_name_systematic
'L-leucyl-L-tyrosylglycylglycylglycine cucurbit[8]uril complex hydrate'
_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'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2023-12-15
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2023-12-16 deposited with the CCDC.	2024-03-08 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90.7510(10)
_cell_angle_gamma                90
_cell_formula_units_Z            1
_cell_length_a                   34.6961(3)
_cell_length_b                   14.63880(10)
_cell_length_c                   18.86300(10)
_cell_measurement_reflns_used    43860
_cell_measurement_temperature    99.99(10)
_cell_measurement_theta_max      75.9140
_cell_measurement_theta_min      2.5410
_cell_volume                     9579.87(12)
_computing_cell_refinement       'CrysAlisPro 1.171.42.102a (Rigaku OD, 2023)'
_computing_data_collection       'CrysAlisPro 1.171.42.102a (Rigaku OD, 2023)'
_computing_data_reduction        'CrysAlisPro 1.171.42.102a (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_pressure         100
_diffrn_ambient_temperature      99.99(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.997
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
  1  \w    -82.00   0.00   0.50    1.35    --  -46.89 108.00 131.00  164
  2  \w     21.00  84.00   0.50    1.35    --   46.89-108.00  34.00  126
  3  \w   -162.00 -82.00   0.50    5.38    --  -91.75-108.00  34.00  160
  4  \w    -82.00 -22.00   0.50    5.38    --  -91.75 108.00 131.00  120
  5  \w    104.00 177.00   0.50    5.38    --  106.92 108.00 131.00  146
  6  \w     37.00 107.00   0.50    5.38    --  106.92-108.00  34.00  140
  7  \w   -119.00 -30.00   0.50    1.35    --  -46.89 -54.00 114.49  178
  8  \w    -30.00  29.00   0.50    1.35    --  -46.89  19.00   0.00  118
  9  \w   -119.00 -83.00   0.50    1.35    --  -46.89 -57.00-120.00   72
 10  \w   -119.00 -83.00   0.50    1.35    --  -46.89 -57.00-150.00   72
 11  \w    -43.00  27.00   0.50    1.35    --  -46.89  37.00  90.00  140
 12  \w     83.00 119.00   0.50    1.35    --   46.89  57.00-150.00   72
 13  \w     83.00 119.00   0.50    1.35    --   46.89  57.00-180.00   72
 14  \w    -51.00 -19.00   0.50    5.38    --  -91.75  45.00 -90.00   64
 15  \w    -71.00 -19.00   0.50    5.38    --  -91.75  61.00  90.00  104
 16  \w   -164.00 -77.00   0.50    5.38    --  -91.75 -45.00  63.98  174
 17  \w    -51.00 -19.00   0.50    5.38    --  -91.75  45.00 120.00   64
 18  \w    -51.00 -19.00   0.50    5.38    --  -91.75  45.00 -60.00   64
 19  \w   -162.00 -88.00   0.50    5.38    --  -91.75-125.00-150.00  148
 20  \w   -164.00 -83.00   0.50    5.38    --  -91.75 -57.00-162.59  162
 21  \w   -164.00-100.00   0.50    5.38    --  -91.75 -94.00 -90.00  128
 22  \w    -51.00 -19.00   0.50    5.38    --  -91.75  45.00  90.00   64
 23  \w    -51.00 -19.00   0.50    5.38    --  -91.75  45.00 -30.00   64
 24  \w   -164.00 -91.00   0.50    5.38    --  -91.75 -61.00 -30.00  146
 25  \w   -164.00 -91.00   0.50    5.38    --  -91.75 -61.00 -60.00  146
 26  \w     37.00 112.00   0.50    5.38    --  106.92-125.00   0.00  150
 27  \w     34.00 106.00   0.50    5.38    --  106.92 -94.00 -90.00  144
 28  \w     37.00 112.00   0.50    5.38    --  106.92-125.00 120.00  150
 29  \w     34.00  71.00   0.50    5.38    --  106.92 -61.00  90.00   74
 30  \w     36.00 107.00   0.50    5.38    --  106.92-105.00-111.01  142
 31  \w     34.00  71.00   0.50    5.38    --  106.92 -61.00 -60.00   74
 32  \w     34.00  71.00   0.50    5.38    --  106.92 -61.00   0.00   74
 33  \w     37.00 112.00   0.50    5.38    --  106.92-125.00-120.00  150
 34  \w     37.00 112.00   0.50    5.38    --  106.92-125.00 150.00  150
 35  \w     93.00 178.00   0.50    5.38    --  106.92  45.00-150.00  170
 36  \w     34.00 106.00   0.50    5.38    --  106.92 -94.00  30.00  144
 37  \w     95.00 177.00   0.50    5.38    --  106.92 125.00 -30.00  164
 38  \w     34.00  71.00   0.50    5.38    --  106.92 -61.00-120.00   74
 39  \w   -119.00 -32.00   0.50    1.35    --  -46.89 -48.00 -95.05  174
 40  \w   -119.00 -32.00   0.50    1.35    --  -46.89 -48.00  33.66  174
 41  \w   -119.00 -32.00   0.50    1.35    --  -46.89 -52.00-159.34  174
 42  \w   -119.00 -71.00   0.50    1.35    --  -46.89 -55.00 -36.40   96
 43  \w   -119.00 -30.00   0.50    1.35    --  -46.89 -54.00  -4.10  178
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0435630000
_diffrn_orient_matrix_UB_12      0.0117996000
_diffrn_orient_matrix_UB_13      0.0117671000
_diffrn_orient_matrix_UB_21      0.0031903000
_diffrn_orient_matrix_UB_22      0.1017859000
_diffrn_orient_matrix_UB_23      -0.0198646000
_diffrn_orient_matrix_UB_31      -0.0079289000
_diffrn_orient_matrix_UB_32      -0.0239635000
_diffrn_orient_matrix_UB_33      -0.0783742000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0443
_diffrn_reflns_av_unetI/netI     0.0300
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       42
_diffrn_reflns_limit_h_min       -42
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -17
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            88713
_diffrn_reflns_point_group_measured_fraction_full 0.995
_diffrn_reflns_point_group_measured_fraction_max 0.989
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         70.000
_diffrn_reflns_theta_min         4.020
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.948
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.68547
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.102a (Rigaku Oxford Diffraction, 2023)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.367
_exptl_crystal_description       plank
_exptl_crystal_F_000             4131
_exptl_crystal_recrystallization_method 'pH 7 10 mM phosphate-buffered D2O'
_exptl_crystal_size_max          0.12
_exptl_crystal_size_mid          0.08
_exptl_crystal_size_min          0.04
_refine_diff_density_max         0.700
_refine_diff_density_min         -0.340
_refine_diff_density_rms         0.064
_refine_ls_abs_structure_details
;
 Refined as an inversion twin.
;
_refine_ls_abs_structure_Flack   0.2(2)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.069
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1317
_refine_ls_number_reflns         17957
_refine_ls_number_restraints     14
_refine_ls_restrained_S_all      1.069
_refine_ls_R_factor_all          0.0590
_refine_ls_R_factor_gt           0.0560
_refine_ls_shift/su_max          0.004
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0350P)^2^+25.0000P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1308
_refine_ls_wR_factor_ref         0.1324
_reflns_Friedel_coverage         0.904
_reflns_Friedel_fraction_full    0.991
_reflns_Friedel_fraction_max     0.980
_reflns_number_gt                16856
_reflns_number_total             17957
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc01122h2.cif
_cod_data_source_block           hpd817c
_cod_depositor_comments
'Adding full bibliography for 1571239--1571240.cif.'
_cod_original_formula_sum        'C276 H381.40 N148 O132.20'
_cod_database_code               1571240
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C H N O'
_chemical_oxdiff_usercomment     'H-LYGGG-OH Q8'
_shelx_estimated_absorpt_t_max   0.963
_shelx_estimated_absorpt_t_min   0.895
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.84081
 0.15919
2. Restrained distances
 H31B-O32
 1.95 with sigma of 0.02
 H26A-O21A
 2.1 with sigma of 0.02
 H26A-O22A
 2.05 with sigma of 0.02
 O19_$1-H34D
 2.2 with sigma of 0.02
 H35C-O10
 2.1 with sigma of 0.02
 H31A-O21B
 2.15 with sigma of 0.02
 H36-N36
 0.85 with sigma of 0.02
 H34E-O13_$1
 2.05 with sigma of 0.02
 H25-O24
 2 with sigma of 0.02
 O20-H28B
 2 with sigma of 0.02
 H27A-O22B
 1.7 with sigma of 0.02
 H27C-O23A
 1.95 with sigma of 0.02
 H27C-O27A
 1.05 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(C69B) = Uanis(O23B) = Uanis(O23A) = Uanis(C69A) = Uanis(O22A) = Uanis(C68)
Uanis(O22B) = Uanis(C69B) = Uanis(O23B)
Uanis(O27B) = Uanis(O27A)
4. Others
 Fixed Sof: O21A(0.6) O35(0.75) H35C(0.75) O31(0.5) H31A(0.5) H31B(0.5)
 O22A(0.6) O23A(0.6) H68A(0.6) H68B(0.6) H68C(0.4) H68D(0.4) O26(0.5) H26A(0.5)
 O32(0.5) C69A(0.6) C69B(0.4) O23B(0.4) O21B(0.4) O22B(0.4) O27A(0.5) O27B(0.3)
 H27C(0.5) H27A(0.3) H27B(0.3)
5.a Free rotating group:
 O33(H33B,H33C), O34(H34D,H34E), O29(H29C,H29D), O24(H24C,H24D), O30(H30),
 O28(H28A,H28B), O25(H25), O35(H35C), O31(H31A,H31B), O26(H26A), O27B(H27C,H27A,
 H27B)
5.b Ternary CH refined with riding coordinates:
 C60(H60), C49(H49), C20(H20), C2(H2), C14(H14), C27(H27), C33(H33), C3(H3),
 C15(H15), C45(H45), C9(H9), C44(H44), C26(H26), C21(H21), C8(H8), C58(H58),
 C39(H39), C32(H32), C38(H38)
5.c Secondary CH2 refined with riding coordinates:
 N37(H37A,H37B), C59(H59A,H59B), C24(H24A,H24B), C64(H64A,H64B), C11(H11A,
 H11B), C6(H6A,H6B), C5(H5A,H5B), C42(H42A,H42B), C66(H66A,H66B), C50(H50A,
 H50B), C48(H48A,H48B), C12(H12A,H12B), C35(H35A,H35B), C41(H41A,H41B),
 C23(H23A,H23B), C18(H18A,H18B), C29(H29A,H29B), C47(H47A,H47B), C17(H17A,H17B),
  C30(H30A,H30B), C36(H36A,H36B), C68(H68A,H68B), C68(H68C,H68D)
5.d Aromatic/amide H refined with riding coordinates:
 N35(H35), C56(H56), C55(H55), C52(H52), C53(H53)
5.e Idealised Me refined as rotating group:
 N34(H34A,H34B,H34C), C61(H61A,H61B,H61C), C62(H62A,H62B,H62C)
5.f Idealised tetrahedral OH refined as rotating group:
 O17(H17)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_olex2_exptl_crystal_mounting_method 'nylon loop'
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.387
_oxdiff_exptl_absorpt_empirical_full_min 0.659