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Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288 nonapeptide T4P variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MRE PDB ENTRY 3MRE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 12% PEG 6000, 0.1M NaCacodylate, 0.1M NaCl, 7.5mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.622 α = 90 b = 79.392 β = 112.02 c = 55.661 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 ADSC QUANTUM 4 2006-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93300 ESRF ID14-2
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 2.3 50 99.3 0.11 11.8 3.74 18522 -3 23.69
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 2.3 2.38 97.6 0.401 3.6
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 PDB ENTRY 3MRE 2.3 15 17664 1782 95.29 0.189 0.186 0.1898 0.257 0.2013 RANDOM 17.549
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] -0.49 -1.25 -0.96 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.485 r_dihedral_angle_4_deg 17.468 r_dihedral_angle_3_deg 14.162 r_dihedral_angle_1_deg 6.24 r_scangle_it 2.358 r_mcangle_it 1.578 r_scbond_it 1.525 r_angle_refined_deg 1.142 r_mcbond_it 0.864 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.485 r_dihedral_angle_4_deg 17.468 r_dihedral_angle_3_deg 14.162 r_dihedral_angle_1_deg 6.24 r_scangle_it 2.358 r_mcangle_it 1.578 r_scbond_it 1.525 r_angle_refined_deg 1.142 r_mcbond_it 0.864 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3138 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction AMoRE phasing