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High resolution crystal structure of the MHC class I complex H-2Kb/SEV9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAB PDB entry 2vab 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 3.08 60.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.287 α = 90 b = 88.342 β = 90 c = 45.322 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 IMAGE PLATE MARRESEARCH 2000-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979 SSRL BL9-1
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 1.7 32 99.7 0.056 14.9 3.7 60060 -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 1.7 1.73 99.9 0.591 1.4 3.7 2991
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 2vab chains A and B 1.71 32 54406 2890 95.7 0.18761 0.18671 0.196 0.20431 0.2116 RANDOM 21.198
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] -0.74 1.34 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.04 r_scangle_it 5.076 r_dihedral_angle_1_deg 4.734 r_scbond_it 3.054 r_angle_other_deg 2.559 r_mcangle_it 1.989 r_angle_refined_deg 1.784 r_mcbond_it 1.088 r_nbtor_other 0.411 r_symmetry_hbond_refined 0.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.04 r_scangle_it 5.076 r_dihedral_angle_1_deg 4.734 r_scbond_it 3.054 r_angle_other_deg 2.559 r_mcangle_it 1.989 r_angle_refined_deg 1.784 r_mcbond_it 1.088 r_nbtor_other 0.411 r_symmetry_hbond_refined 0.229 r_nbd_refined 0.222 r_nbd_other 0.21 r_symmetry_hbond_other 0.19 r_symmetry_vdw_other 0.179 r_xyhbond_nbd_refined 0.169 r_symmetry_vdw_refined 0.155 r_chiral_restr 0.153 r_xyhbond_nbd_other 0.036 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.001 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3112 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing