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X-ray structure of the adduct formed upon reaction of cisplatin with human angiogenin after 1 month soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ANG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10% PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.25 α = 90 b = 37.51 β = 90 c = 38.16 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2021-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.769 42.63 95.3 0.082 0.996 17.1 10 10455
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.02 98.1 0.566 0.927 2.4 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.99 42.625 8525 380 96.056 0.31 0.3077 0.3137 0.3672 0.3774 23.288
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.078 -0.067 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.607 r_dihedral_angle_4_deg 20.804 r_dihedral_angle_3_deg 20.063 r_dihedral_angle_1_deg 7.551 r_lrange_it 4.919 r_lrange_other 4.868 r_mcangle_it 2.706 r_mcangle_other 2.704 r_scangle_it 2.371 r_scangle_other 2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.607 r_dihedral_angle_4_deg 20.804 r_dihedral_angle_3_deg 20.063 r_dihedral_angle_1_deg 7.551 r_lrange_it 4.919 r_lrange_other 4.868 r_mcangle_it 2.706 r_mcangle_other 2.704 r_scangle_it 2.371 r_scangle_other 2.37 r_mcbond_it 1.71 r_mcbond_other 1.71 r_angle_refined_deg 1.526 r_scbond_it 1.501 r_scbond_other 1.5 r_angle_other_deg 1.197 r_symmetry_xyhbond_nbd_refined 0.31 r_nbd_other 0.25 r_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.21 r_nbd_refined 0.198 r_nbtor_refined 0.161 r_symmetry_nbd_refined 0.137 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 976 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing