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Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide G4M-V5W variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MRG PDB ENTRY 3MRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 9% PEG 6000, 0.1M NaCitrate, 0.1M NaCl, 5mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.407 α = 90 b = 80.506 β = 112.44 c = 55.904 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 315r 2007-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.1 50 99.5 0.107 8.71 3.73 25056 -3 31.747
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 2.1 2.17 99.9 0.46 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 3MRG 2.1 15 24988 2499 100 0.239 0.239 0.2415 0.296 0.2435 RANDOM 39.034
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] -0.18 -4.05 -3.43 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.643 r_dihedral_angle_4_deg 19.33 r_dihedral_angle_3_deg 17.266 r_dihedral_angle_1_deg 6.245 r_scangle_it 2.603 r_scbond_it 1.613 r_angle_refined_deg 1.305 r_mcangle_it 1.176 r_mcbond_it 0.68 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.643 r_dihedral_angle_4_deg 19.33 r_dihedral_angle_3_deg 17.266 r_dihedral_angle_1_deg 6.245 r_scangle_it 2.603 r_scbond_it 1.613 r_angle_refined_deg 1.305 r_mcangle_it 1.176 r_mcbond_it 0.68 r_nbtor_refined 0.301 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3155 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction AMoRE phasing