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CRYSTAL STRUCTURE OF HLA-B*2709 COMPLEXED WITH THE LATENT MEMBRANE PROTEIN 2 PEPTIDE (LMP2) OF EPSTEIN-BARR VIRUS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K5N PDB ENTRY 1K5N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1M TRIS, PH 8.5, 21% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.9 56.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.92 α = 90 b = 82.595 β = 104.35 c = 62.79 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH 2003-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 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 1.72 60 99 0.045 20 3.3 53353 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 1.72 1.78 96 0.262 4 2.6
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 PDB ENTRY 1K5N 1.71 60.86 50633 2703 98.9 0.156 0.154 0.1654 0.19 0.1931 RANDOM 13.13
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] -0.59 -0.12 0.08 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.118 r_scangle_it 4.371 r_scbond_it 2.695 r_mcangle_it 1.715 r_angle_refined_deg 1.586 r_mcbond_it 0.965 r_angle_other_deg 0.902 r_symmetry_vdw_other 0.336 r_nbd_other 0.26 r_nbd_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.118 r_scangle_it 4.371 r_scbond_it 2.695 r_mcangle_it 1.715 r_angle_refined_deg 1.586 r_mcbond_it 0.965 r_angle_other_deg 0.902 r_symmetry_vdw_other 0.336 r_nbd_other 0.26 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.102 r_nbtor_other 0.085 r_symmetry_vdw_refined 0.079 r_bond_refined_d 0.015 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3183 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing