Design of a Zn-based porphyrin MOF biosensor for fluorometric detection of HER2 as a breast cancer biomarker
Ibrahim, May R.; Alneyadi, Shaikha; Truong, Khai-Nghi; Maghraby, Hesham El-; Abdellah, Mohamed; El-Zohry, Ahmed M.; Wuttke, Stefan; Greish, Yaser; RSC Advances 15 (2025) 21479–21492; doi:10.1039/D5RA01942G

data_7250584
_publ_section_title
;
 Design of a Zn-based porphyrin MOF biosensor for fluorometric detection
 of HER2 as a breast cancer biomarker
;
_journal_issue                   27
_journal_name_full               'RSC Advances'
_journal_page_first              21479
_journal_page_last               21492
_journal_paper_doi               10.1039/D5RA01942G
_journal_volume                  15
_journal_year                    2025
_chemical_formula_moiety         'C48 H28 N4 O10 Zn3 [+solvent]'
_chemical_formula_sum            'C48 H28 N4 O10 Zn3'
_chemical_formula_weight         1016.91
_chemical_name_common            ZnTCPP
_chemical_name_systematic        'Zinc tetrakis(4-carboxyphenyl)porphyrin'
_space_group_crystal_system      monoclinic
_space_group_IT_number           10
_space_group_name_Hall           '-P 2y'
_space_group_name_H-M_alt        'P 1 2/m 1'
_atom_sites_solution_hydrogens   mixed
_audit_creation_date             2024-02-19
_audit_creation_method
;
Olex2 1.5-ac6-017
(compiled 2024.02.01 svn.r2f8d729c for Rigaku Oxford Diffraction, GUI svn.r6920)
;
_audit_update_record
;
2024-02-19 deposited with the CCDC.	2025-06-04 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 100.1(9)
_cell_angle_gamma                90
_cell_formula_units_Z            1
_cell_length_a                   6.6(2)
_cell_length_b                   16.60(14)
_cell_length_c                   12.4(2)
_cell_measurement_reflns_used    731
_cell_measurement_temperature    100.15
_cell_measurement_theta_max      0.8850
_cell_measurement_theta_min      0.0740
_cell_volume                     1337(5)
_computing_cell_refinement       'CrysAlisPro 1.171.43.80a (Rigaku OD, 2023)'
_computing_data_collection
'CrysAlisPro system (CCD 43.80a 64-bit (release 27-07-2023))'
_computing_data_reduction        'CrysAlisPro 1.171.43.80a (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 1.5-ac6-017 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac6-017 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2014/4 (Sheldrick, 2014)'
_diffrn_ambient_temperature      100.15
_diffrn_detector                 'hybrid pixel electron counting detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix-ED
_diffrn_measured_fraction_theta_full 0.989
_diffrn_measured_fraction_theta_max 0.990
_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    -60.00  60.00   0.25    0.25    --    0.00   0.00   0.00  480
  2  \w    -62.00  62.00   0.25    0.25    --    0.00   0.00   0.00  496
;
_diffrn_measurement_device       'electron diffractometer'
_diffrn_measurement_device_type
'XtaLAB Synergy-ED, HyPix-ED, electron source at 200keV'
_diffrn_measurement_method       'continuous rotation electron diffraction'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0031591000
_diffrn_orient_matrix_UB_12      0.0002972000
_diffrn_orient_matrix_UB_13      -0.0013979000
_diffrn_orient_matrix_UB_21      0.0017210000
_diffrn_orient_matrix_UB_22      0.0012392000
_diffrn_orient_matrix_UB_23      -0.0005748000
_diffrn_orient_matrix_UB_31      0.0014586000
_diffrn_orient_matrix_UB_32      -0.0008136000
_diffrn_orient_matrix_UB_33      -0.0013905000
_diffrn_radiation_probe          electron
_diffrn_radiation_type           electron
_diffrn_radiation_wavelength     0.0251
_diffrn_reflns_av_R_equivalents  0.2453
_diffrn_reflns_av_unetI/netI     0.1866
_diffrn_reflns_Laue_measured_fraction_full 0.989
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       20
_diffrn_reflns_limit_k_min       -20
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            14152
_diffrn_reflns_point_group_measured_fraction_full 0.989
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        0.863
_diffrn_reflns_theta_max         0.899
_diffrn_reflns_theta_min         0.073
_diffrn_source                   'electron diffractometer'
_exptl_absorpt_coefficient_mu    0.000
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.12419
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.80a (Rigaku Oxford Diffraction, 2023)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear red'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    red
_exptl_crystal_density_diffrn    1.260
_exptl_crystal_description       plate
_exptl_crystal_F_000             208
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: DMF/EtOH'
_refine_diff_density_max         0.791
_refine_diff_density_min         -0.417
_refine_diff_density_rms         0.065
_refine_ls_extinction_coef       879(21)
_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   1.979
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     155
_refine_ls_number_reflns         2805
_refine_ls_number_restraints     254
_refine_ls_restrained_S_all      2.011
_refine_ls_R_factor_all          0.2286
_refine_ls_R_factor_gt           0.1932
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.4314
_refine_ls_wR_factor_ref         0.4478
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1805
_reflns_number_total             2805
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ra01942g2.cif
_cod_data_source_block           zntcpp
_cod_original_cell_volume        1332(54)
_cod_database_code               7250584
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C48 H28 N4 O10 Zn3'
_diffrn_oxdiff_scatteringfactors_ed
;
UCLA (2022) https://srv.mbi.ucla.edu/faes/data
;
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H,H) groups
2. Restrained distances
 H3A-O3
 1.03 with sigma of 0.02
 O3-H3B
 1.03 with sigma of 0.02
 H3B-H3A
 1.5 with sigma of 0.02
 Zn2-H3B
 2.6 with sigma of 0.02
 Zn2-H3A
 2.6 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 2A with sigma of 0.001 and sigma
for terminal atoms of 0.001 within 2A
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.a Riding coordinates:
 C5(H3A), C5(H3B)
5.b Aromatic/amide H refined with riding coordinates:
 C1(H1), C5(H5), C7(H7), C8(H8), C10(H10), C11(H11)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 66 electrons were 
found in a volume of 463\%A^3^ in 2 voids per unit cell. 
This is consistent with the presence of 
1[C3H7NO] and 1[C2H6O] per unit cell which account for 
66 electrons per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              41393
_shelx_fab_checksum              16868
_olex2_submission_original_sample_id ZnTCPP
_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 4.201
_oxdiff_exptl_absorpt_empirical_full_min 0.349