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Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A1M B*1501/LEKARGSTY Complex without Peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 0.2M NH4Ac, 0.1M tri-Sodium Citrate dihydrate, pH 5.6, 30% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.359 α = 90 b = 81.389 β = 90 c = 109.969 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 MAR scanner 345 mm plate 2004-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.84140 EMBL/DESY, HAMBURG BW7B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.776 31.654 97.44 0.068 14.2 3.7 43204 -3 17.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.87 83.32 0.298 2.5 3.7 19646
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT B*1501/LEKARGSTY Complex without Peptide 1.788 19.083 43303 41032 2172 94.756 0.18 0.17968 0.17695 0.1849 0.23151 0.2373 RANDOM 20.306
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.732 r_dihedral_angle_4_deg 17.408 r_dihedral_angle_3_deg 13.855 r_dihedral_angle_1_deg 6.004 r_scangle_it 3.749 r_scbond_it 2.354 r_mcangle_it 1.498 r_angle_refined_deg 1.437 r_mcbond_it 0.973 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.732 r_dihedral_angle_4_deg 17.408 r_dihedral_angle_3_deg 13.855 r_dihedral_angle_1_deg 6.004 r_scangle_it 3.749 r_scbond_it 2.354 r_mcangle_it 1.498 r_angle_refined_deg 1.437 r_mcbond_it 0.973 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3147 Nucleic Acid Atoms Solvent Atoms 595 Heterogen Atoms 20
Software Software Software Name Purpose SCALA data scaling REFMAC refinement CCP4 data scaling