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Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GSO PDB ENTRY 3GSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 17% PEG 6000, 0.1M NaCitrate, 0.05M NaCl, 5mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.12 α = 90 b = 80.87 β = 112.33 c = 56.2 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 2005-12-02 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 1.3 20 97.2 0.125 10.15 4.53 104890 -3 18.12
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 1.3 1.4 87.3 0.313 2.8
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 3GSO 1.3 15 101798 10272 94.56 0.18 0.179 0.1799 0.202 0.1853 RANDOM 15.863
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] -0.14 -0.36 -0.23 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.026 r_dihedral_angle_4_deg 15.836 r_dihedral_angle_3_deg 12.93 r_dihedral_angle_1_deg 5.593 r_scangle_it 2.531 r_scbond_it 1.718 r_mcangle_it 1.716 r_angle_refined_deg 1.231 r_mcbond_it 0.997 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.026 r_dihedral_angle_4_deg 15.836 r_dihedral_angle_3_deg 12.93 r_dihedral_angle_1_deg 5.593 r_scangle_it 2.531 r_scbond_it 1.718 r_mcangle_it 1.716 r_angle_refined_deg 1.231 r_mcbond_it 0.997 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3144 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 13
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction AMoRE phasing