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The crystal structure of H-2Db complexed with a partial peptide epitope suggests an MHC Class I assembly-intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CE6 PDB ENTRY 1CE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 25% PEG 6000, 100MM AMMONIUM SULFATE, 100 MM SODIUM CHLORIDE, 50 MM MES PH 5.0
Crystal Properties Matthews coefficient Solvent content 2.89 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.996 α = 90 b = 58.45 β = 106.77 c = 73.534 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 100 CCD MARRESEARCH 1997-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX7.2 SRS PX7.2
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 2.55 30 95.8 0.05 19.8 2.5 15880 1
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 2.55 2.61 96.9 0.16 5.3
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 1CE6 2.55 20 15697 1232 96.2 0.2391 0.2391 0.2376 0.2969 0.2942 RANDOM 34.545
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] 11.203 -3.894 10.317 -21.52
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.15332 c_scangle_it 2.748 c_mcangle_it 2.305 c_scbond_it 1.81 c_mcbond_it 1.355 c_angle_deg 1.33067 c_improper_angle_d 0.76967 c_bond_d 0.007055 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.15332 c_scangle_it 2.748 c_mcangle_it 2.305 c_scbond_it 1.81 c_mcbond_it 1.355 c_angle_deg 1.33067 c_improper_angle_d 0.76967 c_bond_d 0.007055 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3116 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR phasing CNS phasing CNS refinement