☰ Navigation Tabs
Crystal structure of Fab bound to the WT1-derived RMF peptide presented by HLA-A*02:01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W51 HLA-A*02:01 experimental model PDB 6W51 Beta-2 microglobulin in silico model AlphaFold Q2L_Fab_heavy chain in silico model AlphaFold Q2L_Fab_light chain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295.15 8% (w/v) PEG 5000 MME, 5% (v/v) Tacsimate TM (pH 7.0), 100mM HEPES (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 3.21 61.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.07 α = 90 b = 132.81 β = 90 c = 185.66 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295.15 PIXEL DECTRIS EIGER X 9M 2024-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.03 29.92 99.83 0.998 16.9 13.5 49217 90.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.03 3.138 0.99
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 3.03 29.92 1.35 49217 1997 99.97 0.1851 0.183 0.1856 0.2338 0.2333 88.25
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 18.3854 f_angle_d 1.3973 f_chiral_restr 0.0777 f_bond_d 0.0135 f_plane_restr 0.0083
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12830 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing