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Crystal Structure of a disulfide trapped single chain trimer composed of the MHC I heavy chain H-2Kb Y84C E63A mutant, beta-2microglobulin, and ovalbumin-derived peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QRI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.2M Am sulphate, 25% PEG 4K, 0.1M Na cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.82 56.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.13 α = 90 b = 90.19 β = 111.22 c = 89.45 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 PILATUS3 S 6M 2013-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.0000 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 42.52 97.9 11.6 3.8 38095
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 2QRI 2.4 42.517 1.36 38073 1902 97.69 0.2034 0.2005 0.2003 0.2595 0.2585
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 6.361 f_angle_d 0.541 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6292 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling MOLREP phasing