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Crystal structure of HLA*02:01 with the 11-mer TP53 peptide GLAPPQHLIRV
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 Screen MCSG4 - condition C9:
0.1 M Bis-Tris Propane:HCl and 60% (v/v) Microlytic mix;
(Microlytic mix: 1.8305 M Malonic Acid, 0.25 M Ammonium Citrate Tribasic, 0.12 M Succinic Acid, 0.3 M DL-Malic Acid, 0.4 M Sodium Acetate Trihydrate, 0.5 M Sodium Formate, 0.16 M Ammonium Tartrate Dibasic)
Crystal Properties Matthews coefficient Solvent content 6.85 82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.13 α = 90 b = 161.13 β = 90 c = 330.28 γ = 120
Symmetry Space Group P 63 2 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 EIGER2 XE 9M 2024-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97857 NSLS-II 19-ID
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 3.25 48 99.8 0.197 0.206 0.058 0.989 9.5 12.4 40748 64.24
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 3.25 3.31 99.9 1.142 0.369 0.741 1.6 10
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.25 47.97 1.34 40644 2036 99.59 0.1949 0.194 0.1938 0.2117 0.2114 67.91
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.1266 f_angle_d 0.5006 f_chiral_restr 0.0385 f_plane_restr 0.0048 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6280 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 60
Software Software Software Name Purpose HKL-3000 data scaling PHENIX refinement HKL-3000 data reduction HKL-3000 phasing