☰ Navigation Tabs
MHC CLASS I NATURAL MUTANT H-2KBM8 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 6.40, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.31 α = 90 b = 87.35 β = 90 c = 45.17 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 CUSTOM-MADE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 1.8 19.9 93.8 0.074 21.9 4.2 47714 47714 2.4 16
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 1.8 1.82 95.4 0.494 2.4 4.1 1601
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. 1.8 19.9 45593 3473 89.5 0.197 0.197 0.2 0.211 0.2156 RANDOM 26.2
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] -1.53 1.98 -0.44
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_scangle_it 2.48 c_mcangle_it 1.57 c_scbond_it 1.56 c_angle_deg 1.5 c_improper_angle_d 1.2 c_mcbond_it 0.95 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3118 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 67
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing