Bioorthogonal site-selective conjugation of fluorescent dyes to antibodies: method and potential applications
Grossenbacher, Philipp; Essers, Maria C.; Moser, Joël; Singer, Simon A.; Häusler, Stephanie; Stieger, Bruno; Rougier, Jean-Sébastien; Lochner, Martin; RSC Advances 12 (2022) 28306–28317; doi:10.1039/D2RA05580E

data_7245629
_publ_section_title
;
 Bioorthogonal site-selective conjugation of fluorescent dyes to
 antibodies: method and potential applications
;
_journal_issue                   44
_journal_name_full               'RSC Advances'
_journal_page_first              28306
_journal_page_last               28317
_journal_paper_doi               10.1039/D2RA05580E
_journal_volume                  12
_journal_year                    2022
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C14 H19 N3 O5 S'
_chemical_formula_sum            'C14 H19 N3 O5 S'
_chemical_formula_weight         341.38
_chemical_name_common            Biotin-NHS
_chemical_name_systematic
'2,5-dioxopyrrolidin-1-yl 5-((3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoate'
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_symmetry_cell_setting           monoclinic
_symmetry_Int_Tables_number      4
_symmetry_space_group_name_Hall  'P 2yb'
_symmetry_space_group_name_H-M   'P 1 21 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2022-06-06T20:11:31-00:00
_audit_update_record
;
2022-06-07 deposited with the CCDC.	2022-09-27 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 91.9565(8)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   5.16670(4)
_cell_length_b                   7.62474(6)
_cell_length_c                   20.29901(17)
_cell_measurement_reflns_used    26371
_cell_measurement_temperature    173.00(10)
_cell_measurement_theta_max      79.792
_cell_measurement_theta_min      2.178
_cell_volume                     799.208(11)
_computing_cell_refinement       'CrysAlisPro 1.171.41.117a (Rigaku OD, 2021)'
_computing_data_collection       'CrysAlisPro 1.171.41.117a (Rigaku OD, 2021)'
_computing_data_reduction        'CrysAlisPro 1.171.41.117a (Rigaku OD, 2021)'
_computing_molecular_graphics    'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3 (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_temperature      173.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 1
_diffrn_measured_fraction_theta_max 0.999
_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    -39.00  50.00   0.50    0.20    --  -23.00  59.00  17.00  178
  2  \w    -94.00  -7.00   0.50    0.20    --  -23.00 -59.00-122.00  174
  3  \w    -23.00  64.00   0.50    0.20    --   47.92 -59.00-122.00  174
  4  \w     32.00 120.00   0.50    0.20    --   47.92  59.00  17.00  176
  5  \w     98.00 177.00   0.50    1.25    --  113.25  59.00  17.00  158
  6  \w    -95.00   0.00   0.50    0.20    --  -23.00 -77.00  60.00  190
  7  \w    -70.00 -12.00   0.50    0.20    --  -23.00 125.00  60.00  116
  8  \w    -70.00 -12.00   0.50    0.20    --  -23.00 125.00 120.00  116
  9  \w      9.00  42.00   0.50    0.20    --   38.00  91.00  57.42   66
 10  \w     25.00 121.00   0.50    0.20    --   47.92  77.00-150.00  192
 11  \w     -1.00  81.00   0.50    0.20    --   47.92 -99.00  90.00  164
 12  \w     32.00 126.00   0.50    0.20    --   54.00  76.00 158.38  188
 13  \w     32.00 126.00   0.50    0.20    --   54.00  76.00 -75.77  188
 14  \w     35.00 131.00   0.50    0.20    --   58.00  77.00 -31.53  192
 15  \w     40.00 135.00   0.50    0.20    --   62.00  75.00-169.79  190
 16  \w     40.00 135.00   0.50    0.20    --   62.00  76.00  -1.96  190
 17  \w     39.00 135.00   0.50    0.20    --   62.00  77.00 107.23  192
 18  \w     39.00 135.00   0.50    0.20    --   62.00  77.00  46.82  192
 19  \w     39.00 135.00   0.50    0.20    --   62.00  77.00-150.36  192
 20  \w     40.00 135.00   0.50    0.20    --   62.00  75.00 -72.71  190
 21  \w     44.00 139.00   0.50    0.20    --   66.00  76.00 151.70  190
 22  \w     44.00 139.00   0.50    0.20    --   66.00  75.00  65.99  190
 23  \w     48.00 143.00   0.50    0.20    --   70.00  75.00-132.36  190
 24  \w     55.00 143.00   0.50    0.20    --   70.00  56.00-177.14  176
 25  \w     58.00 151.00   0.50    0.20    --   78.00  70.00-130.22  186
 26  \w     71.00 162.00   0.50    1.25    --   90.00  68.00  94.53  182
 27  \w     97.00 177.00   0.50    1.25    --  113.25  61.00 -60.00  160
 28  \w     97.00 177.00   0.50    1.25    --  113.25  61.00 150.00  160
 29  \w     97.00 177.00   0.50    1.25    --  113.25  61.00   0.00  160
 30  \w     97.00 177.00   0.50    1.25    --  113.25  61.00 -30.00  160
 31  \w     42.00 106.00   0.50    1.25    --  113.25 -94.00  90.00  128
 32  \w     97.00 177.00   0.50    1.25    --  113.25  61.00-180.00  160
 33  \w     91.00 177.00   0.50    1.25    --  113.25  77.00 -30.00  172
 34  \w     97.00 177.00   0.50    1.25    --  113.25  61.00-120.00  160
 35  \w     42.00  68.00   0.50    1.25    --  113.25 -61.00-120.00   52
 36  \w     91.00 177.00   0.50    1.25    --  113.25  77.00  90.00  172
 37  \w     91.00 177.00   0.50    1.25    --  113.25  77.00-150.00  172
 38  \w     42.00 106.00   0.50    1.25    --  113.25 -94.00 -90.00  128
 39  \w     91.00 177.00   0.50    1.25    --  113.25  77.00  30.00  172
 40  \w     42.00 106.00   0.50    1.25    --  113.25 -94.00 -30.00  128
 41  \w     97.00 177.00   0.50    1.25    --  113.25  61.00 -90.00  160
 42  \w     97.00 177.00   0.50    1.25    --  113.25  61.00  90.00  160
 43  \w     91.00 177.00   0.50    1.25    --  113.25  77.00-120.00  172
 44  \w     91.00 177.00   0.50    1.25    --  113.25  77.00 120.00  172
 45  \w    101.00 177.00   0.50    1.25    --  113.25  45.00 -60.00  152
 46  \w     97.00 177.00   0.50    1.25    --  113.25  61.00-150.00  160
 47  \w     97.00 177.00   0.50    1.25    --  113.25  61.00  30.00  160
 48  \w     42.00 106.00   0.50    1.25    --  113.25 -94.00-150.00  128
 49  \w     42.00 102.00   0.50    1.25    --  113.25 -77.00  30.00  120
 50  \w     42.00  68.00   0.50    1.25    --  113.25 -61.00  90.00   52
 51  \w     42.00 106.00   0.50    1.25    --  113.25 -94.00  60.00  128
 52  \w     42.00 106.00   0.50    1.25    --  113.25 -94.00 150.00  128
 53  \w     91.00 177.00   0.50    1.25    --  113.25  77.00   0.00  172
 54  \w     42.00 106.00   0.50    1.25    --  113.25 -94.00 120.00  128
 55  \w     97.00 177.00   0.50    1.25    --  113.25  61.00 120.00  160
 56  \w     42.00 102.00   0.50    1.25    --  113.25 -77.00-180.00  120
 57  \w     97.00 177.00   0.50    1.25    --  113.25  61.00  60.00  160
 58  \w     91.00 177.00   0.50    1.25    --  113.25  77.00 150.00  172
 59  \w     42.00 102.00   0.50    1.25    --  113.25 -77.00 -30.00  120
 60  \w     42.00 102.00   0.50    1.25    --  113.25 -77.00-120.00  120
 61  \w     42.00 102.00   0.50    1.25    --  113.25 -77.00  60.00  120
 62  \w     91.00 177.00   0.50    1.25    --  113.25  77.00-180.00  172
 63  \w     42.00  68.00   0.50    1.25    --  113.25 -61.00 150.00   52
 64  \w     42.00  68.00   0.50    1.25    --  113.25 -61.00 120.00   52
 65  \w     42.00 106.00   0.50    1.25    --  113.25 -94.00 -60.00  128
 66  \w     42.00 106.00   0.50    1.25    --  113.25 -94.00   0.00  128
 67  \w     25.00 121.00   0.50    0.20    --   47.92  77.00 -30.00  192
 68  \w     27.00 122.00   0.50    0.20    --   50.00  77.00 143.38  190
 69  \w     31.00 126.00   0.50    0.20    --   54.00  77.00  47.29  190
 70  \w     32.00 126.00   0.50    0.20    --   54.00  76.00  96.18  188
 71  \w     44.00 115.00   0.50    0.20    --   62.00  66.00 -28.76  142
 72  \w     45.00 139.00   0.50    0.20    --   66.00  72.00 -34.13  188
 73  \w     58.00 142.00   0.50    0.20    --   70.00  42.00 108.41  168
;
_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      -0.2271555
_diffrn_orient_matrix_UB_12      0.0936967
_diffrn_orient_matrix_UB_13      0.0324073
_diffrn_orient_matrix_UB_21      0.0471026
_diffrn_orient_matrix_UB_22      0.1637106
_diffrn_orient_matrix_UB_23      -0.04238
_diffrn_orient_matrix_UB_31      -0.1878063
_diffrn_orient_matrix_UB_32      -0.0723315
_diffrn_orient_matrix_UB_33      -0.0540082
_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  0.0497
_diffrn_reflns_av_unetI/netI     0.0538
_diffrn_reflns_Laue_measured_fraction_full 1
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -9
_diffrn_reflns_limit_l_max       25
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            31548
_diffrn_reflns_point_group_measured_fraction_full 1
_diffrn_reflns_point_group_measured_fraction_max 0.995
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         77.681
_diffrn_reflns_theta_min         2.178
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.072
_exptl_absorpt_correction_T_max  1
_exptl_absorpt_correction_T_min  0.87592
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
        CrysAlisPro 1.171.41.117a (Rigaku Oxford Diffraction, 2021)
        Empirical absorption correction using spherical harmonics,
        implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'light colourless'
_exptl_crystal_density_diffrn    1.419
_exptl_crystal_description       plate
_exptl_crystal_F_000             360
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: dichloromethane/methanol'
_exptl_crystal_size_max          0.215
_exptl_crystal_size_mid          0.094
_exptl_crystal_size_min          0.033
_refine_diff_density_max         0.176
_refine_diff_density_min         -0.152
_refine_diff_density_rms         0.032
_refine_ls_abs_structure_details
;
 Flack x determined using 1513 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.004(11)
_refine_ls_extinction_coef       0.0029(8)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.059
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     217
_refine_ls_number_reflns         3405
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.059
_refine_ls_R_factor_all          0.0277
_refine_ls_R_factor_gt           0.0273
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0439P)^2^+0.1359P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0734
_refine_ls_wR_factor_ref         0.0737
_reflns_Friedel_coverage         0.849
_reflns_Friedel_fraction_full    0.999
_reflns_Friedel_fraction_max     0.99
_reflns_number_gt                3357
_reflns_number_total             3405
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2ra05580e3.cif
_cod_data_source_block           22ML008_PG01-080-02-02
_cod_database_code               7245629
_shelx_estimated_absorpt_t_min   0.678
_shelx_estimated_absorpt_t_max   0.938
_oxdiff_exptl_absorpt_empirical_details
;
        Empirical correction (ABSPACK) includes:
        - Absorption correction using spherical harmonics
        - Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 2.029
_oxdiff_exptl_absorpt_empirical_full_min 0.77
_shelx_shelxl_version_number     2018/3
_olex2_refinement_description
;
        1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
        2.a Ternary CH refined with riding coordinates:
 C3(H3), C2(H2A), C5(H5)
        2.b Secondary CH2 refined with riding coordinates:
 C7(H7A,H7B), C8(H8A,H8B), C13(H13A,H13B), C9(H9A,H9B), C6(H6A,H6B), C4(H4A,
 H4B), C12(H12A,H12B)
;
_shelx_res_checksum              90030