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_1571239
_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_formula_moiety         'C48 H48 N32 O16, C21 H31 N5 O7, 18(H2 O), H O'
_chemical_formula_sum            'C69 H116 N37 O42'
_chemical_formula_weight         2135.98
_chemical_name_common            'H-YLGGG-OH Q8 complex hydrate'
_chemical_name_systematic
'L-tyrosyl-L-leucylglycylglycylglycine cucurbit[8]uril complex octadecahydrate'
_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'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2023-11-22
_audit_creation_method
;
Olex2 1.5-ac5-024
(compiled 2022.04.12 svn.rca3783a0 for Rigaku Oxford Diffraction, GUI svn.r6498)
;
_audit_update_record
;
2023-12-08 deposited with the CCDC.	2024-03-08 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 107.2330(10)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   13.11250(10)
_cell_length_b                   21.09440(10)
_cell_length_c                   18.85710(10)
_cell_measurement_reflns_used    80756
_cell_measurement_temperature    100.01(10)
_cell_measurement_theta_max      76.5650
_cell_measurement_theta_min      2.4460
_cell_volume                     4981.73(6)
_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-ac5-024 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac5-024 (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      100.01(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.975
_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    -51.00 -19.00   0.50    0.36    --  -91.75  45.00-180.00   64
  2  \w    -51.00 -19.00   0.50    0.36    --  -91.75  45.00-150.00   64
  3  \w    -51.00 -19.00   0.50    0.36    --  -91.75  45.00-120.00   64
  4  \w    -51.00 -19.00   0.50    0.36    --  -91.75  45.00 -90.00   64
  5  \w    -51.00 -19.00   0.50    0.36    --  -91.75  45.00 -60.00   64
  6  \w    -51.00 -19.00   0.50    0.36    --  -91.75  45.00 -30.00   64
  7  \w    -51.00 -19.00   0.50    0.36    --  -91.75  45.00  30.00   64
  8  \w    -51.00 -19.00   0.50    0.36    --  -91.75  45.00  60.00   64
  9  \w    -51.00 -19.00   0.50    0.36    --  -91.75  45.00  90.00   64
 10  \w    -30.00  29.00   0.50    0.09    --  -46.89  19.00  30.00  118
 11  \w    -43.00  27.00   0.50    0.09    --  -46.89  37.00  60.00  140
 12  \w     27.00  88.00   0.50    0.09    --   46.89-115.00   4.00  122
 13  \w     34.00  94.00   0.50    0.09    --   46.89-125.00 120.00  120
 14  \w     37.00 112.00   0.50    0.36    --  106.92-125.00 -60.00  150
 15  \w     55.00 140.00   0.50    0.36    --  106.92-166.00-141.00  170
 16  \w     37.00 112.00   0.50    0.36    --  106.92-125.00-180.00  150
 17  \w     55.00 122.00   0.50    0.09    --   46.89-166.00-141.00  134
 18  \w     37.00 112.00   0.50    0.36    --  106.92-125.00 -30.00  150
 19  \w     38.00 109.00   0.50    0.36    --  106.92-115.00   4.00  142
 20  \w     37.00 112.00   0.50    0.36    --  106.92-125.00 120.00  150
 21  \w     36.00 106.00   0.50    0.36    --  106.92-102.00 129.76  140
 22  \w     37.00 112.00   0.50    0.36    --  106.92-125.00  30.00  150
 23  \w     34.00 106.00   0.50    0.36    --  106.92 -94.00  30.00  144
 24  \w     34.00 106.00   0.50    0.36    --  106.92 -94.00-180.00  144
 25  \w     34.00 101.00   0.50    0.36    --  106.92 -77.00-180.00  134
 26  \w     34.00  71.00   0.50    0.36    --  106.92 -61.00 -90.00   74
 27  \w     34.00 101.00   0.50    0.36    --  106.92 -77.00  30.00  134
 28  \w     34.00  71.00   0.50    0.36    --  106.92 -61.00  90.00   74
 29  \w     83.00 119.00   0.50    0.09    --   46.89  57.00  60.00   72
 30  \w     69.00 154.00   0.50    0.36    --  106.92 166.00-119.00  170
 31  \w    101.00 178.00   0.50    0.36    --  106.92  77.00-180.00  154
 32  \w     69.00 119.00   0.50    0.09    --   46.89 166.00-119.00  100
 33  \w    101.00 176.00   0.50    0.36    --  106.92 115.00  94.00  150
 34  \w    -83.00 -23.00   0.50    0.36    --  -91.75 115.00  94.00  120
 35  \w    -82.00  -6.00   0.50    0.09    --  -46.89 115.00  94.00  152
 36  \w   -114.00 -33.00   0.50    0.09    --  -46.89 166.00-119.00  162
 37  \w   -114.00 -33.00   0.50    0.36    --  -91.75 166.00-119.00  162
 38  \w   -119.00 -31.00   0.50    0.09    --  -46.89 -53.00 -44.10  176
 39  \w   -119.00 -83.00   0.50    0.09    --  -46.89 -57.00 -90.00   72
 40  \w   -119.00 -83.00   0.50    0.09    --  -46.89 -57.00-120.00   72
 41  \w   -119.00 -83.00   0.50    0.09    --  -46.89 -57.00  90.00   72
 42  \w   -119.00 -83.00   0.50    0.09    --  -46.89 -57.00 120.00   72
 43  \w   -119.00 -83.00   0.50    0.09    --  -46.89 -57.00 150.00   72
 44  \w   -167.00 -74.00   0.50    0.36    --  -91.75 -15.00  60.00  186
 45  \w   -164.00 -77.00   0.50    0.36    --  -91.75 -48.00  17.13  174
 46  \w   -164.00 -91.00   0.50    0.36    --  -91.75 -61.00 -60.00  146
 47  \w   -164.00 -91.00   0.50    0.36    --  -91.75 -61.00 -90.00  146
 48  \w   -164.00 -77.00   0.50    0.36    --  -91.75 -50.00-153.28  174
 49  \w   -164.00-100.00   0.50    0.36    --  -91.75 -94.00 -30.00  128
 50  \w   -161.00 -80.00   0.50    0.36    --  -91.75-115.00   4.00  162
 51  \w   -119.00 -47.00   0.50    0.09    --  -46.89-166.00-141.00  144
 52  \w   -137.00 -47.00   0.50    0.36    --  -91.75-166.00-141.00  180
;
_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      0.0609446000
_diffrn_orient_matrix_UB_12      0.0465715000
_diffrn_orient_matrix_UB_13      0.0607833000
_diffrn_orient_matrix_UB_21      -0.0690658000
_diffrn_orient_matrix_UB_22      0.0550065000
_diffrn_orient_matrix_UB_23      -0.0421976000
_diffrn_orient_matrix_UB_31      -0.0816160000
_diffrn_orient_matrix_UB_32      -0.0118094000
_diffrn_orient_matrix_UB_33      0.0428473000
_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  0.0504
_diffrn_reflns_av_unetI/netI     0.0315
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.975
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       25
_diffrn_reflns_limit_k_min       -25
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            112702
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.953
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         76.955
_diffrn_reflns_theta_min         2.453
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.022
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.293
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.102a (Rigaku Oxford Diffraction, 2023)
Numerical absorption correction based on gaussian integration over
a multifaceted crystal model
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    1.424
_exptl_crystal_description       plate
_exptl_crystal_F_000             2250
_exptl_crystal_recrystallization_method
'phosphate-buffered D2O; heating and cooling cycles'
_exptl_crystal_size_max          0.24
_exptl_crystal_size_mid          0.23
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.772
_refine_diff_density_min         -0.278
_refine_diff_density_rms         0.056
_refine_ls_abs_structure_details
;
 Refined as an inversion twin.
;
_refine_ls_abs_structure_Flack   0.14(10)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.031
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1401
_refine_ls_number_reflns         20089
_refine_ls_number_restraints     2
_refine_ls_restrained_S_all      1.034
_refine_ls_R_factor_all          0.0391
_refine_ls_R_factor_gt           0.0377
_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^)+(0.0552P)^2^+2.5221P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0973
_refine_ls_wR_factor_ref         0.0986
_reflns_Friedel_coverage         0.900
_reflns_Friedel_fraction_full    0.996
_reflns_Friedel_fraction_max     0.929
_reflns_number_gt                19374
_reflns_number_total             20089
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc01122h2.cif
_cod_data_source_block           hpd814c
_cod_depositor_comments
'Adding full bibliography for 1571239--1571240.cif.'
_cod_original_sg_symbol_H-M      'P 21'
_cod_database_code               1571239
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C H N O'
_chemical_oxdiff_usercomment     'Trinity H-YLGGG-OH/08 PO4 buffer D2O'
_shelx_estimated_absorpt_t_max   0.905
_shelx_estimated_absorpt_t_min   0.792
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.86(10)
 0.14(10)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups, All N(H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups, All O(H,H) groups
3. Restrained distances
 HE-O31
 0.95 with sigma of 0.02
4.a Free rotating group:
 O30(H,HA), O24(HB,HC), O31(HD,HE), O32(HG,HH), O36(HI,HJ), O37(HK,HL), O28(HM,
 HN), O38(HO,HP), O49(HQ,HR), O26(HS,HT), O35(HU,HV), O40(HW,HX), O39(HY,HZ),
 O25(H1,H4), O50(H5,H6), O27(H10,H11), O33(H12,H13), O34(H22,H23), O29(H24)
4.b Ternary CH refined with riding coordinates:
 C39(H39), C8(H8), C9(H9), C3(H3), C14(H14), C32(H32), C62(H25), C26(H26),
 C44(H44), C45(H45), C33(H33), C2(H2), C27(H27), C58(H30), C56(H31), C15(H15),
 C21(H21), C38(H38), C20(H20)
4.c Secondary CH2 refined with riding coordinates:
 C47(H47A,H47B), C12(H12A,H12B), C17(H17A,H17B), C36(H36A,H36B), C23(H23A,
 H23B), C57(H28,H29), C18(H18A,H18B), C6(H6A,H6B), C41(H41A,H41B), C42(H42A,
 H42B), C29(H29A,H29B), C24(H24A,H24B), C35(H35A,H35B), C30(H30A,H30B),
 C11(H11A,H11B), C63(H35,H36), C5(H5A,H5B), C48(H48A,H48B), C52(H40,H41),
 C54(H43,H46), C50(H47,H48)
4.d Aromatic/amide H refined with riding coordinates:
 N34(H7), N33(H19), C68(H34), C69(H37), C65(H42), C66(H49)
4.e Idealised Me refined as rotating group:
 N37(H16,H17,H18), C60(H50,H51,H52), C59(H53,H54,H55)
4.f Idealised tetrahedral OH refined as rotating group:
 O23(HF)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              23102
_shelx_fab_checksum              27457
_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
- Detector area scaling
- B-factor correction
;
_oxdiff_exptl_absorpt_empirical_full_max 1.366
_oxdiff_exptl_absorpt_empirical_full_min 0.621