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Crystal Structure of H2-Kb in complex with the chicken ovalbumin epitope OVA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VAC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2M calcium acetate, 15% PEG 8K, 0.1M Na-cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.82 56.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.99 α = 90 b = 90.41 β = 111.71 c = 89.74 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 IMAGE PLATE RIGAKU RAXIS 2008-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2 100 98.1 0.048 19.12 65977 -3 29.362
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 97.1 0.253 0.291 5.7
Refinement Statistics Diffraction ID Structure Solution 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 1vac 2 31.042 0.01 61416 3084 91.43 0.189 0.1861 0.1968 0.2434 0.2465 26.2578
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] -2.2094 -0.8132 8.0957 -5.8863
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.472 f_angle_d 1.042 f_chiral_restr 0.073 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6301 Nucleic Acid Atoms Solvent Atoms 928 Heterogen Atoms 3
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction PHENIX refinement