☰ Navigation Tabs
Crystal structure of HLA-A*2450 complexed with 8-mer model peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F7T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 277 100mM Tris, 20 % PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.08 60.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.239 α = 90 b = 46.46 β = 104.011 c = 141.65 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 4M 2021-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 2.095 50 99.5 0.086 0.997 12.58 3.8 64492
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 2.1 2.22 0.463 0.857
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4F7T 2.09507668635 45.8119360216 1.35400862047 64481 3225 99.4923622898 0.18851052864 0.186412774516 0.1895 0.228090007321 0.2304 37.1007312696
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 14.5507304407 f_angle_d 1.09371840275 f_chiral_restr 0.0568190052346 f_bond_d 0.00896307424595 f_plane_restr 0.00577055260436
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5997 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 199
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling MOLREP phasing