Tracking Super Resolved Structure of Mitochondria using Red Emissive Carbon Nanodots as Fluorescent Biomarker
Garg, Richa; Anjum, Farhan; Salam, Abdul; Kaushik, Kush; Sharma, Shagun; Sahrawat, Udisha; Yadav, Aditya; Nandi, Chayan Kanti; Chemical Communications  (2023) –; doi:10.1039/D3CC03390B

data_7132217
_publ_section_title
;
 Tracking Super Resolved Structure of Mitochondria using Red Emissive
 Carbon Nanodots as Fluorescent Biomarker
;
_journal_name_full               'Chemical Communications'
_journal_paper_doi               10.1039/D3CC03390B
_journal_year                    2023
_chemical_formula_moiety         'C28 H26 N2 P, Br'
_chemical_formula_sum            'C28 H26 Br N2 P'
_chemical_formula_weight         501.39
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2023-09-27
_audit_creation_method
;
Olex2 1.5-ac5-024
(compiled 2022.04.12 svn.rca3783a0 for Rigaku Oxford Diffraction, GUI svn.r6498)
;
_audit_update_record
;
2023-09-30 deposited with the CCDC.	2023-10-17 downloaded from the CCDC.
;
_cell_angle_alpha                99.442(5)
_cell_angle_beta                 104.072(5)
_cell_angle_gamma                91.385(5)
_cell_formula_units_Z            2
_cell_length_a                   9.3394(5)
_cell_length_b                   11.3297(7)
_cell_length_c                   13.5356(8)
_cell_measurement_reflns_used    4253
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      66.2080
_cell_measurement_theta_min      3.4020
_cell_volume                     1367.36(14)
_computing_cell_refinement       'CrysAlisPro 1.171.42.49 (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.42.49 (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.42.49 (Rigaku OD, 2022)'
_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 2018/1 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXD  (Sheldrick, 2008)'
_diffrn_ambient_temperature      293(2)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 15.9974
_diffrn_detector_type            Eos
_diffrn_measured_fraction_theta_full 0.988
_diffrn_measured_fraction_theta_max 0.988
_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      0.00 102.00   1.00    1.00    --   24.78  57.00 -90.00  102
  2  \w     60.00  91.00   1.00    1.00    --   24.78 178.00 150.00   31
  3  \w    -15.00  82.00   1.00    1.00    --   24.78  77.00 150.00   97
  4  \w     37.00  89.00   1.00    1.00    --   24.78  57.00  30.00   52
  5  \w      2.00  36.00   1.00    1.00    --   24.78  57.00  30.00   34
  6  \w     68.00 105.00   1.00    1.00    --   24.78 178.00  60.00   37
  7  \w    100.00 146.00   1.00    1.00    --   66.39 111.00   0.00   46
  8  \w    126.00 152.00   1.00    1.00    --   66.39 111.00 120.00   26
  9  \w    -15.00 106.00   1.00    1.00    --   66.39 -37.00-120.00  121
 10  \w    124.00 149.00   1.00    1.00    --   66.39 111.00  60.00   25
 11  \w     39.00 101.00   1.00    1.00    --   66.39-111.00-120.00   62
 12  \w     15.00 102.00   1.00    1.00    --   66.39-111.00  60.00   87
 13  \w    -23.00 157.00   1.00    1.00    --   66.39 -12.00  30.00  180
 14  \w     -6.00 105.00   1.00    1.00    --   66.39 -63.00  60.00  111
 15  \w     51.00  77.00   1.00    1.00    --   66.39  63.00-150.00   26
 16  \w     95.00 120.00   1.00    1.00    --   66.39  63.00-150.00   25
 17  \w     47.00  91.00   1.00    1.00    --  108.00 -21.00-120.00   44
 18  \w     74.00  99.00   1.00    1.00    --  108.00-104.00 -30.00   25
 19  \w     54.00  80.00   1.00    1.00    --  108.00 -54.00  90.00   26
 20  \w     84.00 110.00   1.00    1.00    --  108.00 -77.00-120.00   26
 21  \w    102.00 177.00   1.00    1.00    --  108.00 104.00-150.00   75
 22  \w     32.00  74.00   1.00    1.00    --  108.00 -65.00 -60.00   42
 23  \w    144.00 177.00   1.00    1.00    --  108.00 104.00-120.00   33
 24  \w    136.00 177.00   1.00    1.00    --  108.00 104.00   0.00   41
 25  \w     68.00 137.00   1.00    1.00    --  108.00  54.00 -60.00   69
 26  \w     21.00  46.00   1.00    1.00    --  108.00-104.00 -30.00   25
 27  \w    142.00 168.00   1.00    1.00    --  108.00 138.00   0.00   26
 28  \w    101.00 153.00   1.00    1.00    --  108.00 104.00 -30.00   52
 29  \w     28.00  86.00   1.00    1.00    --  108.00-104.00-180.00   58
 30  \w     62.00 135.00   1.00    1.00    --  108.00  43.00 150.00   73
 31  \w     92.00 120.00   1.00    1.00    --  108.00 138.00   0.00   28
 32  \w     29.00  91.00   1.00    1.00    --  108.00 -89.00   0.00   62
 33  \w    108.00 152.00   1.00    1.00    --  108.00  54.00 -90.00   44
 34  \w    104.00 177.00   1.00    1.00    --  108.00 104.00 -60.00   73
 35  \w    128.00 178.00   1.00    1.00    --  108.00 138.00  60.00   50
 36  \w     23.00 104.00   1.00    1.00    --  108.00-104.00  60.00   81
 37  \w     87.00 112.00   1.00    1.00    --  108.00 138.00  60.00   25
 38  \w     82.00 107.00   1.00    1.00    --  108.00-104.00  90.00   25
 39  \w     78.00 105.00   1.00    1.00    --  108.00  54.00 -90.00   27
 40  \w     87.00 157.00   1.00    1.00    --  108.00  65.00-120.00   70
 41  \w    101.00 133.00   1.00    1.00    --  108.00 104.00-180.00   32
 42  \w     47.00  74.00   1.00    1.00    --  108.00 -77.00 120.00   27
 43  \w     98.00 124.00   1.00    1.00    --  108.00 -77.00 120.00   26
 44  \w     85.00 110.00   1.00    1.00    --  108.00-104.00 150.00   25
 45  \w     24.00  60.00   1.00    1.00    --  108.00-104.00  90.00   36
 46  \w     42.00  79.00   1.00    1.00    --  108.00 -77.00-120.00   37
 47  \w    112.00 173.00   1.00    1.00    --  108.00  77.00 150.00   61
 48  \w    139.00 165.00   1.00    1.00    --  108.00 -21.00-120.00   26
 49  \w     90.00 159.00   1.00    1.00    --  108.00  65.00   0.00   69
 50  \w     28.00  56.00   1.00    1.00    --  108.00-104.00-120.00   28
 51  \w     87.00 112.00   1.00    1.00    --  108.00-112.00 151.78   25
 52  \w     66.00 110.00   1.00    1.00    --  108.00-112.00 -43.13   44
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Eos'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0414238000
_diffrn_orient_matrix_UB_12      -0.1353079000
_diffrn_orient_matrix_UB_13      -0.0146549000
_diffrn_orient_matrix_UB_21      0.1248737000
_diffrn_orient_matrix_UB_22      -0.0095070000
_diffrn_orient_matrix_UB_23      0.0959309000
_diffrn_orient_matrix_UB_31      -0.1083522000
_diffrn_orient_matrix_UB_32      0.0262242000
_diffrn_orient_matrix_UB_33      0.0691847000
_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  0.0322
_diffrn_reflns_av_unetI/netI     0.0345
_diffrn_reflns_Laue_measured_fraction_full 0.988
_diffrn_reflns_Laue_measured_fraction_max 0.988
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            9585
_diffrn_reflns_point_group_measured_fraction_full 0.988
_diffrn_reflns_point_group_measured_fraction_max 0.988
_diffrn_reflns_theta_full        66.344
_diffrn_reflns_theta_max         66.344
_diffrn_reflns_theta_min         3.419
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.715
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.67380
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.49 (Rigaku Oxford Diffraction, 2022)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            Whitish
_exptl_crystal_density_diffrn    1.218
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       triclinic
_exptl_crystal_F_000             516
_exptl_crystal_size_max          0.419
_exptl_crystal_size_mid          0.264
_exptl_crystal_size_min          0.182
_refine_diff_density_max         1.088
_refine_diff_density_min         -1.798
_refine_diff_density_rms         0.108
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.060
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     289
_refine_ls_number_reflns         4743
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.060
_refine_ls_R_factor_all          0.0850
_refine_ls_R_factor_gt           0.0737
_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^)+(0.1343P)^2^+3.4007P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2253
_refine_ls_wR_factor_ref         0.2422
_reflns_Friedel_coverage         0.000
_reflns_number_gt                3944
_reflns_number_total             4743
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3cc03390b2.cif
_cod_data_source_block           tpp_1_rt_cu
_cod_original_cell_volume        1367.35(15)
_cod_database_code               7132217
_shelx_shelxl_version_number     2018/1
_chemical_oxdiff_formula         'C56  H52  Br4  N4  O4  P2  '
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
2.a Secondary CH2 refined with riding coordinates:
 C9(H9A,H9B), C10(H10A,H10B), C8(H8A,H8B)
2.b Aromatic/amide H refined with riding coordinates:
 N1(H1), C16(H16), C18(H18), C22(H22), C2(H2), C24(H24), C3(H3), C4(H4),
 C28(H28), C15(H15), C20(H20), C26(H26), C19(H19), C12(H12), C5(H5), C14(H14),
 C25(H25), C27(H27), C21(H21), C13(H13)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              32154
_shelx_hkl_checksum              52879
_shelx_fab_checksum              41502
_olex2_date_sample_data_collection 2022-05-31
_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 1.590
_oxdiff_exptl_absorpt_empirical_full_min 0.693