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Structure of the antibody fragment H2 in complex with HLA-A*02:01/p53R175H
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6O4Y 6O4Y, 6UJ9 experimental model PDB 6UJ9 6O4Y, 6UJ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 0.2 M Ammonium chloride, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.21 α = 90 b = 123.69 β = 100.36 c = 136.909 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2020-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97931 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.53 30.37 95.3 0.247 0.311 0.186 0.938 3.6 2.4 43734
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.53 3.66 89.2 0.76 0.96 0.577 0.541 2.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6O4Y, 6UJ9 3.53 30.37 41530 2193 95.06 0.2044 0.2003 0.2012 0.2832 0.2767 RANDOM 61.859
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] -4.22 -0.88 2.89 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.677 r_dihedral_angle_4_deg 21.052 r_dihedral_angle_3_deg 20.051 r_dihedral_angle_1_deg 7.417 r_angle_refined_deg 1.665 r_angle_other_deg 1.382 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.677 r_dihedral_angle_4_deg 21.052 r_dihedral_angle_3_deg 20.051 r_dihedral_angle_1_deg 7.417 r_angle_refined_deg 1.665 r_angle_other_deg 1.382 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25786 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing