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Crystal Structure of HLA-A*2402 Complexed with a Newly Identified Peptide from 2009H1N1 PB1 (496-505)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I6L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 293 0.1 M Bis-Tris and 10% (w/v) polyethylene glycol 3,350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.94 58.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.122 α = 90 b = 64.787 β = 90.04 c = 50.229 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS VII 2010-11-13 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) R Merge I (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 1.9 50 97.9 0.054 0.054 24.4 4 40018
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 95.8 0.512 0.512 2.38 3.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3I6L 1.9 19.69 0.1 38401 1923 93.8 0.186 0.185 0.1814 0.216 0.2064
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] -5.5479 -0.7257 6.8745 -1.3266
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.171 f_angle_d 0.914 f_chiral_restr 0.068 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3122 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling