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Crystal structure of a H5-specific CTL epitope variant derived from H5N1 influenza virus in complex with HLA-A*0201
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JF1 PDB ENTRY 1JF1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 25mM MES(pH 6.5), 16% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.172 α = 90.02 b = 79.304 β = 89.99 c = 86.739 γ = 89.96
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 IMAGE PLATE RIGAKU RAXIS IV++ 2009-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.197 25.535 95.8 23 76982 72653
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.197 2.28 23 2.14
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1JF1 2.197 25.535 2 72549 4117 95.76 0.1943 0.192 0.2367 0.2325 33.185
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] -4.627 -2.014 -0.105 -8.296 0.226 12.923
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.316 f_angle_d 0.817 f_chiral_restr 0.059 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12668 Nucleic Acid Atoms Solvent Atoms 1086 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building PHENIX refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing