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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 PDB ENTRY 1A1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.2M MgAc4H20, 0.1M Na-cacodylate, pH 6.5, 20% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.582 α = 90 b = 81.891 β = 90 c = 110.408 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 CCD MARRESEARCH 2004-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-5 0.96900 MAX II I911-5
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 2.3 19.44 93.19 0.104 5.1 3.8 20977 19549 -3 29.855
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 2.3 2.42 96.29 0.339 1.9 3.8 2868
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUHGOUT PDB ENTRY 1A1M 2.3 19.437 20977 19549 997 93.19 0.173 0.173 0.169 0.245 0.2323 RANDOM 23.975
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 33.454 r_dihedral_angle_4_deg 21.807 r_dihedral_angle_3_deg 17.5 r_dihedral_angle_1_deg 7.302 r_scangle_it 5.026 r_scbond_it 3.209 r_mcangle_it 2.058 r_angle_refined_deg 1.889 r_mcbond_it 1.333 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.454 r_dihedral_angle_4_deg 21.807 r_dihedral_angle_3_deg 17.5 r_dihedral_angle_1_deg 7.302 r_scangle_it 5.026 r_scbond_it 3.209 r_mcangle_it 2.058 r_angle_refined_deg 1.889 r_mcbond_it 1.333 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.133 r_bond_refined_d 0.022 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3155 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 29
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling