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Crystal structure of HLA-B*2709 complexed with a variant of the latent membrane protein 2 peptide (LMP2(L)) of epstein-barr virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UXS PDB entry 1uxs
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 20% PEG 4000, 0.1M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.53 51.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.753 α = 90 b = 82.56 β = 90 c = 108.993 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 MAR CCD 165 mm 2006-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 1.74 50 98.1 0.069 7.5 58060 46874 1 2
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 1.74 1.8 85.2 0.396
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 PDB entry 1uxs 1.74 24.02 47677 44448 2367 98.12 0.19404 0.19199 0.1896 0.23251 0.2292 RANDOM 16.257
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 -0.06 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.867 r_dihedral_angle_4_deg 14.014 r_dihedral_angle_3_deg 13.084 r_dihedral_angle_1_deg 8.49 r_sphericity_free 2.264 r_scangle_it 1.963 r_scbond_it 1.402 r_sphericity_bonded 1.236 r_angle_refined_deg 1.189 r_rigid_bond_restr 1.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.867 r_dihedral_angle_4_deg 14.014 r_dihedral_angle_3_deg 13.084 r_dihedral_angle_1_deg 8.49 r_sphericity_free 2.264 r_scangle_it 1.963 r_scbond_it 1.402 r_sphericity_bonded 1.236 r_angle_refined_deg 1.189 r_rigid_bond_restr 1.077 r_mcangle_it 0.979 r_mcbond_it 0.718 r_nbtor_refined 0.296 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.101 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.093 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3184 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOLREP phasing