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Crystal structure of HLA-B*3508 presenting EBV peptide EPLPQGQLTAY at 1.7A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 277 0.2M Ammonium acetate, 0.1M Cacodylate (pH7.7), 16% PEG 3350, pH 7.6, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.55 51.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.832 α = 90 b = 81.661 β = 90 c = 110.328 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 100 IMAGE PLATE RIGAKU RAXIS 2003-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.502
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 1.7 65.653 97.7 0.046 0.046 11 3.8 50052
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) 1.7 1.79 94.9 0.404 0.404 1.9 3.7 6979
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 1ZSD 1.7 22.01 49994 2520 97.51 0.203 0.201 0.1962 0.236 0.2322 RANDOM 22.661
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.206 r_dihedral_angle_4_deg 22.103 r_dihedral_angle_3_deg 13.131 r_scangle_it 6.072 r_dihedral_angle_1_deg 6.005 r_scbond_it 4.201 r_mcangle_it 2.843 r_mcbond_it 1.991 r_angle_refined_deg 1.442 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.206 r_dihedral_angle_4_deg 22.103 r_dihedral_angle_3_deg 13.131 r_scangle_it 6.072 r_dihedral_angle_1_deg 6.005 r_scbond_it 4.201 r_mcangle_it 2.843 r_mcbond_it 1.991 r_angle_refined_deg 1.442 r_nbtor_refined 0.301 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.167 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3214 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction CCP4 data scaling