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Crystal Structure of a SARS Corona Virus Derived Peptide Bound to the Human Major Histocompatibility Complex Class I molecule HLA-B*1501
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 273 0.2M Magnesium chloride hexahydrate, 0.1M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.53 51.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.658 α = 90 b = 81.713 β = 90 c = 109.391 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 CCD MAR CCD 165 mm 2006-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-5 MAX II I911-5
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 1.87 18.29 99.8 0.064 15.7 4 38220 1 10.47
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) 1.87 1.97 100 0.362 3.1 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1XR9 1.87 18.29 38305 36303 1910 99.8 0.19 0.188 0.1873 0.227 0.2264 RANDOM 25.82
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] -0.7 -0.69 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.889 r_dihedral_angle_4_deg 17.821 r_dihedral_angle_3_deg 14.563 r_dihedral_angle_1_deg 6.424 r_scangle_it 4.09 r_scbond_it 2.582 r_mcangle_it 1.748 r_angle_refined_deg 1.501 r_mcbond_it 1.179 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.889 r_dihedral_angle_4_deg 17.821 r_dihedral_angle_3_deg 14.563 r_dihedral_angle_1_deg 6.424 r_scangle_it 4.09 r_scbond_it 2.582 r_mcangle_it 1.748 r_angle_refined_deg 1.501 r_mcbond_it 1.179 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3184 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 28
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction