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Crystal Structure of HLA B*3508 in complex with a HCMV 8-mer peptide from the pp65 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 277 0.2M ammonium acetate, 16% PEG 3350, pH 7.6, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.59 52.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.995 α = 90 b = 81.738 β = 90 c = 111.096 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 2005-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
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 1.3 50 96 0.035 0.035 48.1 6.6 109900 17.648
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) 1.3 76.1 0.231 0.231 4.4
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 3BW9 1.3 15 104238 5523 95.79 0.18995 0.18895 0.1916 0.20886 0.2127 RANDOM 17.74
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] -0.21 -0.01 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.645 r_dihedral_angle_4_deg 17.549 r_dihedral_angle_3_deg 11.849 r_dihedral_angle_1_deg 5.636 r_scangle_it 1.731 r_mcangle_it 1.395 r_scbond_it 1.345 r_angle_refined_deg 1.132 r_mcbond_it 0.882 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.645 r_dihedral_angle_4_deg 17.549 r_dihedral_angle_3_deg 11.849 r_dihedral_angle_1_deg 5.636 r_scangle_it 1.731 r_mcangle_it 1.395 r_scbond_it 1.345 r_angle_refined_deg 1.132 r_mcbond_it 0.882 r_nbtor_refined 0.314 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.221 r_symmetry_hbond_refined 0.218 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.082 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3652 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction