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Mhc Class I H-2Kb molecule complexed with pKB1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VAC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.5M K2HPO4/N2HPO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.24 α = 90 b = 90.63 β = 111.51 c = 89.58 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH 1999-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 2.3 22.53 99.5 0.046 11.4 3.3 43653 43653
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) 2.3 2.42 98.9 0.161 4.2 2.5 6306
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1VAC 2.3 12 42902 42902 4278 0.211 0.211 0.207 0.2055 0.259 0.2334 RANDOM 40.57
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] -4.9 0.3 12.1 -6.7
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 24.2 p_staggered_tor 17.9 p_scangle_it 3.17 p_planar_tor 2.2 p_scbond_it 2.03 p_mcangle_it 2.02 p_mcbond_it 1.11 p_chiral_restr 0.14 p_planar_d 0.027 p_angle_d 0.022
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 24.2 p_staggered_tor 17.9 p_scangle_it 3.17 p_planar_tor 2.2 p_scbond_it 2.03 p_mcangle_it 2.02 p_mcbond_it 1.11 p_chiral_restr 0.14 p_planar_d 0.027 p_angle_d 0.022 p_plane_restr 0.011 p_bond_d 0.009 p_hb_or_metal_coord p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6318 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling