☰ Navigation Tabs
High resolution crystal structure of the MHC class I complex H-2Kb/VSV8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAA PDB entry 2vaa, chains A and B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 K/NA PHOSPHATE, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.086 α = 90 b = 88.121 β = 90 c = 45.24 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 2001-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.033 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 42 92.5 0.113 9.8 6.3 81282 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 71.5 0.431 2.9 3.7 6180
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2vaa, chains A and B 1.5 41.89 74678 3977 96.85 0.18552 0.18432 0.1937 0.20814 0.2197 RANDOM 17.187
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] -0.41 0.55 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.108 r_scangle_it 4.609 r_dihedral_angle_1_deg 4.602 r_angle_other_deg 3.173 r_scbond_it 2.755 r_mcangle_it 1.902 r_angle_refined_deg 1.643 r_mcbond_it 1.008 r_nbtor_other 0.434 r_symmetry_vdw_other 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.108 r_scangle_it 4.609 r_dihedral_angle_1_deg 4.602 r_angle_other_deg 3.173 r_scbond_it 2.755 r_mcangle_it 1.902 r_angle_refined_deg 1.643 r_mcbond_it 1.008 r_nbtor_other 0.434 r_symmetry_vdw_other 0.299 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.216 r_xyhbond_nbd_other 0.204 r_nbd_other 0.201 r_chiral_restr 0.169 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.12 r_bond_refined_d 0.014 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3121 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing