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MHC CLASS I NATURAL MUTANT H-2KBM1 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND SENDAI VIRUS NUCLEOPROTEIN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAA pdb-entry 2vaa without peptide, water, and mutated side chains truncated to alanine.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 290 K/Na phosphate, MPD , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.75 α = 90 b = 87.92 β = 90 c = 45.99 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.7 23.3 99.5 0.045 34.4 4.3 61624 61624 3.5 20.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.72 99.8 0.456 3.5 4.1 2029
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION CNS, done by rigid body refinement
of starting model. THROUGHOUT pdb-entry 2vaa without peptide, water, and mutated side
chains truncated to alanine. 1.7 23.3 59620 4548 96.2 0.204 0.204 0.2114 0.213 0.2208 RANDOM 24.2
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] -1.47 2.08 -0.61
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.4 c_scangle_it 2.29 c_angle_deg 1.5 c_mcangle_it 1.5 c_scbond_it 1.42 c_improper_angle_d 1.12 c_mcbond_it 0.9 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3123 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 86
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing