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MHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGNYPAW
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 sodium/potassium phosphate buffer 1.9M, MPD 1%, glycerol (cryoprotection)
Crystal Properties Matthews coefficient Solvent content 2.84 56.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.933 α = 90 b = 136.665 β = 90 c = 45.231 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 315r 2012-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0000 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 73.948 99.9 0.106 0.123 0.061 9.1 3.8 37692 37692 34.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 100 0.623 0.623 0.361 1.2 3.9 5408
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2vab 2 42.98 37651 1885 99.82 0.2026 0.2009 0.2345 0.2224 RANDOM 28.105
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] 0.08 0.07 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.578 r_dihedral_angle_4_deg 13.622 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 5.881 r_mcangle_it 2.443 r_mcbond_it 1.522 r_mcbond_other 1.522 r_angle_refined_deg 1.053 r_angle_other_deg 0.681 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.578 r_dihedral_angle_4_deg 13.622 r_dihedral_angle_3_deg 12.34 r_dihedral_angle_1_deg 5.881 r_mcangle_it 2.443 r_mcbond_it 1.522 r_mcbond_other 1.522 r_angle_refined_deg 1.053 r_angle_other_deg 0.681 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3126 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 52
Software Software Software Name Purpose SCALA data scaling XDS data scaling REFMAC refinement Coot model building PDB_EXTRACT data extraction