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Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide C6V 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 15% PEG 6000, 0.1M NaCitrate, 3.6mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.634 α = 90 b = 80.973 β = 113.17 c = 57.019 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 2006-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97569 ESRF ID14-4
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 2.4 50 93.9 0.133 7.82 2.99 16618 -3 40.304
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 2.4 2.48 90.2 0.553 2.9
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 2.41 15 15691 1599 90.88 0.205 0.2 0.2045 0.279 0.2135 RANDOM 31.59
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] 0.33 -1.28 -1.23 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.645 r_dihedral_angle_4_deg 18.935 r_dihedral_angle_3_deg 17.882 r_dihedral_angle_1_deg 5.99 r_scangle_it 2.909 r_mcangle_it 1.988 r_scbond_it 1.843 r_angle_refined_deg 1.223 r_mcbond_it 1.064 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.645 r_dihedral_angle_4_deg 18.935 r_dihedral_angle_3_deg 17.882 r_dihedral_angle_1_deg 5.99 r_scangle_it 2.909 r_mcangle_it 1.988 r_scbond_it 1.843 r_angle_refined_deg 1.223 r_mcbond_it 1.064 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3145 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction AMoRE phasing