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X-ray structure of the adduct formed upon reaction of cisplatin with human angiogenin after 5 days 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 5.1 293 10% PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate
Crystal Properties Matthews coefficient Solvent content 2.16 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.32 α = 90 b = 37.48 β = 90 c = 38.33 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 1.76 42.66 95 0.083 1 19.1 10.7 12229
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 1.76 1.79 83.2 0.636 0.856 2.3 6.4
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 1.76 42.66 12114 619 94.893 0.245 0.243 0.2511 0.2905 0.298 20.824
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] -0.149 -0.049 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.606 r_dihedral_angle_4_deg 17.403 r_dihedral_angle_3_deg 16.088 r_dihedral_angle_1_deg 8.04 r_lrange_it 6.535 r_lrange_other 6.52 r_scangle_it 4.093 r_scangle_other 4.092 r_mcangle_other 3.464 r_mcangle_it 3.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.606 r_dihedral_angle_4_deg 17.403 r_dihedral_angle_3_deg 16.088 r_dihedral_angle_1_deg 8.04 r_lrange_it 6.535 r_lrange_other 6.52 r_scangle_it 4.093 r_scangle_other 4.092 r_mcangle_other 3.464 r_mcangle_it 3.46 r_scbond_it 2.577 r_scbond_other 2.561 r_mcbond_it 2.177 r_mcbond_other 2.151 r_angle_refined_deg 1.724 r_angle_other_deg 1.353 r_symmetry_xyhbond_nbd_refined 0.259 r_nbd_other 0.232 r_nbd_refined 0.191 r_symmetry_nbd_other 0.187 r_symmetry_nbd_refined 0.164 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 985 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing