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X-ray structure of the adduct formed upon reaction of oxaliplatin with human angiogenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 298 10 % PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate
Crystal Properties Matthews coefficient Solvent content 1.94 36.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.72 α = 90 b = 85.89 β = 90 c = 33.39 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 2020-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.86 42.945 99.9 0.171 0.052 0.995 10.5 11.8 9691
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.89 100 1.22 0.387 0.803 2.5 10.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FREE R-VALUE 5EOP 1.86 42.94 9325 463 96.923 0.182 0.1782 0.1893 0.2537 0.2588 25.6
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] 0.037 -0.334 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.772 r_dihedral_angle_3_deg 17.12 r_dihedral_angle_4_deg 15.451 r_lrange_it 8.444 r_lrange_other 8.443 r_dihedral_angle_1_deg 6.54 r_scangle_it 5.264 r_scangle_other 5.261 r_mcangle_it 3.932 r_mcangle_other 3.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.772 r_dihedral_angle_3_deg 17.12 r_dihedral_angle_4_deg 15.451 r_lrange_it 8.444 r_lrange_other 8.443 r_dihedral_angle_1_deg 6.54 r_scangle_it 5.264 r_scangle_other 5.261 r_mcangle_it 3.932 r_mcangle_other 3.929 r_scbond_it 3.283 r_scbond_other 3.255 r_mcbond_it 2.415 r_mcbond_other 2.413 r_angle_refined_deg 1.628 r_angle_other_deg 1.372 r_symmetry_nbd_refined 0.231 r_symmetry_xyhbond_nbd_refined 0.226 r_nbd_other 0.206 r_xyhbond_nbd_refined 0.197 r_nbd_refined 0.194 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.164 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 976 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing