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X-ray crystal structure of HLA-DRA1*0101/DRB5*0101 complexed with a peptide from Epstein Barr Virus DNA polymerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FV1 SINGLE COPY OF 1FV1 (A AND B CHAINS) MINUS PEPTIDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 3.5 14% PEG 3550, 100MM GLYCINE AND 10MM TRIS AT PH 3.5-4.0.
Crystal Properties Matthews coefficient Solvent content 2.54 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.244 α = 90 b = 179.244 β = 90 c = 92.884 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD ADSC CCD MIRRORS 2001-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 3.1 20 94.5 0.414 5.7 6 28750
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 3.1 3.3 78.9 0.774 1.1 1.6
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 SINGLE COPY OF 1FV1 (A AND B CHAINS) MINUS PEPTIDE 3.1 19.88 28750 1415 93 0.256 0.256 0.24 0.31 0.2886 RANDOM 60.6
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] 2.37 12.75 2.37 -4.74
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.1 c_scangle_it 5.9 c_mcangle_it 4.35 c_scbond_it 3.54 c_mcbond_it 2.52 c_angle_deg 1.5 c_improper_angle_d 0.92 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.1 c_scangle_it 5.9 c_mcangle_it 4.35 c_scbond_it 3.54 c_mcbond_it 2.52 c_angle_deg 1.5 c_improper_angle_d 0.92 c_bond_d 0.008 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 6320 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 70
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing