Lighting up RNA-specific multi-photon and super-resolution imaging using a novel zinc complex.
Feng, Zhihui; Zhang, Dongxue; Guo, Hui; Su, Wenqing; Tian, Yupeng; Tian, Xiaohe; Nanoscale 15 (2023) 5486–5493; doi:10.1039/d2nr05392f

data_1568544
_publ_section_title
;
 Lighting up RNA-specific multi-photon and super-resolution imaging using
 a novel zinc complex.
;
_journal_issue                   11
_journal_name_full               Nanoscale
_journal_page_first              5486
_journal_page_last               5493
_journal_paper_doi               10.1039/d2nr05392f
_journal_volume                  15
_journal_year                    2023
_chemical_formula_moiety         'C50 H56 N10 S2 Zn, 4(N O3), 0.6[H2O], 2[H2O]'
_chemical_formula_sum            'C50 H56 N14 O12 S2 Zn'
_chemical_formula_weight         1174.57
_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   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2022-09-07
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2022-09-07 deposited with the CCDC.	2023-02-13 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 129.632(5)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   45.81(2)
_cell_length_b                   9.357(4)
_cell_length_c                   34.484(16)
_cell_measurement_reflns_used    2247
_cell_measurement_temperature    296(2)
_cell_measurement_theta_max      17.154
_cell_measurement_theta_min      2.252
_cell_volume                     11384(9)
_computing_cell_refinement       'SAINT v7.68A (Bruker, 2009)'
_computing_data_reduction        'SAINT v7.68A (Bruker, 2009)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/2 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXS-97 (Sheldrick, 1990)'
_diffrn_ambient_temperature      296.15
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device_type  'CCD area detector'
_diffrn_measurement_method       'phi and omega scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.1231
_diffrn_reflns_av_unetI/netI     0.1221
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       54
_diffrn_reflns_limit_h_min       -54
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       39
_diffrn_reflns_limit_l_min       -41
_diffrn_reflns_number            39361
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        25.000
_diffrn_reflns_theta_max         25.000
_diffrn_reflns_theta_min         1.533
_diffrn_source_current           30.0
_diffrn_source_power             1.5
_diffrn_source_voltage           50.0
_exptl_absorpt_coefficient_mu    0.576
_exptl_absorpt_correction_T_max  0.8935
_exptl_absorpt_correction_T_min  0.8461
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   SADABS
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.371
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       block
_exptl_crystal_F_000             4896
_exptl_crystal_size_max          0.3
_exptl_crystal_size_mid          0.2
_exptl_crystal_size_min          0.2
_refine_diff_density_max         0.462
_refine_diff_density_min         -0.547
_refine_diff_density_rms         0.067
_refine_ls_extinction_coef       0.00023(5)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2019/2 (Sheldrick 2019)'
_refine_ls_goodness_of_fit_ref   0.915
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     832
_refine_ls_number_reflns         9983
_refine_ls_number_restraints     614
_refine_ls_restrained_S_all      1.084
_refine_ls_R_factor_all          0.1602
_refine_ls_R_factor_gt           0.0648
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0809P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1442
_refine_ls_wR_factor_ref         0.1742
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4613
_reflns_number_total             9983
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2nr05392f2.cif
_cod_data_source_block           a
_cod_depositor_comments          'Adding full bibliography for 1568544.cif.'
_cod_database_code               1568544
_shelx_shelxl_version_number     2019/2
_shelx_estimated_absorpt_t_max   0.893
_shelx_estimated_absorpt_t_min   0.846
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 N4-C25
 1.47 with sigma of 0.01
 O5A-N12A \\sim O3A-N12A \\sim O4A-N12A
 with sigma of 0.02
 O5-N12 \\sim O3-N12 \\sim O4-N12
 with sigma of 0.02
 O3-O4 \\sim O3-O5 \\sim O4-O5
 with sigma of 0.02
 O3A-O4A \\sim O3A-O5A \\sim O4A-O5A
 with sigma of 0.02
 N14-O1 \\sim N14A-O1A
 with sigma of 0.02
 O1-O2 \\sim O1-O12 \\sim O2-O12
 with sigma of 0.02
 N4-H25A \\sim N4-H25B \\sim N4-H25C \\sim H25A-H25B \\sim H25A-H25C \\sim
H25B-H25C
 with sigma of 0.04
 O1-N14 \\sim O12-N14 \\sim O2-N14
 with sigma of 0.02
 C25-N4 \\sim C25-H25A \\sim C25-H25B \\sim C25-H25C
 with sigma of 0.02
 N14-O2 \\sim N14A-O2A
 with sigma of 0.02
 O1-O2 \\sim O1A-O2A
 with sigma of 0.04
 N14-O12 \\sim N14A-O12A
 with sigma of 0.02
 O1-O12 \\sim O1A-O12A
 with sigma of 0.04
 O2-O12 \\sim O2A-O12A
 with sigma of 0.04
 O9-O10 \\sim O9-O11 \\sim O10-O11
 with sigma of 0.02
 O11A-N11A \\sim O9A-N11A \\sim O10A-N11A
 with sigma of 0.02
 O10-N11 \\sim O9-N11 \\sim O11-N11
 with sigma of 0.02
 O10A-N11A \\sim O9A-N11A \\sim O11A-N11A
 with sigma of 0.02
 O9A-O10A \\sim O9A-O11A \\sim O10A-O11A
 with sigma of 0.02
 O6-N13 \\sim O8-N13 \\sim O7-N13
 with sigma of 0.02
 O6-O7 \\sim O6-O8 \\sim O7-O8
 with sigma of 0.02
3. Restrained planarity
 O3, N12, O4, O5
 with sigma of 0.1
 O5A, N12A, O4A, O3A
 with sigma of 0.1
 O12, N14, O1, O2
 with sigma of 0.1
 O1A, O2A, N14A, O12A
 with sigma of 0.1
 O10, N11, O9, O11
 with sigma of 0.1
 O10A, O9A, N11A, O11A
 with sigma of 0.1
 O7, N13, O8, O6
 with sigma of 0.1
4. Uiso/Uaniso restraints and constraints
O3 \\sim N12 \\sim O4 \\sim O5 \\sim O5A \\sim N12A \\sim O4A \\sim O3A: within
2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
O12A \\sim O2A \\sim N14A \\sim O1A \\sim O2 \\sim N14 \\sim O1 \\sim O12:
within 2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
O10 \\sim N11 \\sim O9 \\sim O11 \\sim O10A \\sim O9A \\sim N11A \\sim O11A:
within 2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
O9A \\sim N11A \\sim O11A \\sim O10A \\sim O10 \\sim N11 \\sim O9 \\sim O11:
within 2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
N13 \\sim O7 \\sim O8 \\sim O6: within 2A with sigma of 0.01 and sigma for
terminal atoms of 0.02 within 2A
5. Rigid body (RIGU) restrains
 O3, N12, O4, O5
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
 O5A, N12A, O4A, O3A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
 O12A, O2A, N14A, O1A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
 O12, N14, O1, O2
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
 O10A, O9A, N11A, O11A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
 O10, N11, O9, O11
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
 O9A, N11A, O11A, O10A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
 O7, N13, O8, O6
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
6. Others
 Sof(O5A)=Sof(N12A)=Sof(O4A)=Sof(O3A)=1-FVAR(1)
 Sof(N12)=Sof(O4)=Sof(O3)=Sof(O5)=FVAR(1)
 Sof(O2A)=Sof(O12A)=Sof(N14A)=Sof(O1A)=1-FVAR(2)
 Sof(N14)=Sof(O1)=Sof(O2)=Sof(O12)=FVAR(2)
 Sof(O9A)=Sof(N11A)=Sof(O11A)=Sof(O10A)=1-FVAR(3)
 Sof(N11)=Sof(O9)=Sof(O11)=Sof(O10)=FVAR(3)
7.a Secondary CH2 refined with riding coordinates:
 C23(H23A,H23B), C22(H22A,H22B), C48(H48A,H48B), C47(H47A,H47B)
7.b Aromatic/amide H refined with riding coordinates:
 C33(H33), C7(H7), C15(H15), C9(H9), C35(H35), C1(H1), C12(H12), C4(H4),
 C2(H2), C39(H39), C30(H30), C27(H27), C18(H18), C17(H17), C40(H40), C52(H52),
 C43(H43), C28(H28), C3(H3), C38(H38), C42(H42), C29(H29), C13(H13), C14(H14)
7.c Idealised Me refined as rotating group:
 C24(H24A,H24B,H24C), C21(H21A,H21B,H21C), C25(H25A,H25B,H25C), C49(H49A,H49B,
 H49C), C26(H26A,H26B,H26C), C45(H45A,H45B,H45C), C50(H50A,H50B,H50C), C51(H51A,
 H51B,H51C)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 204 electrons were 
found in a volume of 916\%A^3^ in 2 voids per unit cell. 
This is consistent with the presence of 
0.6[H2O], 2[H2O] per Asymmetric Unit 
which account for 208 electrons 
per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              64150
_shelx_fab_checksum              65409
_olex2_submission_special_instructions 'No special instructions were received'