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Crystal Structure of HLA B*3508 in complex with a HCMV 12-mer peptide from the pp65 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H6P
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 2.58 52.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.006 α = 90 b = 82.086 β = 90 c = 111.515 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 1.72 50 98.2 0.057 0.057 27.4 2.1 94441 23.78
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) 1.72 1.82 92.2 0.334 0.334 3.4
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 2H6P 1.75 15 47354 2395 98.85 0.192 0.189 0.1926 0.235 0.2385 RANDOM 23.782
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.063 r_dihedral_angle_4_deg 19.511 r_dihedral_angle_3_deg 14.493 r_dihedral_angle_1_deg 5.905 r_scangle_it 2.335 r_scbond_it 1.744 r_mcangle_it 1.668 r_angle_refined_deg 1.278 r_mcbond_it 1.077 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.063 r_dihedral_angle_4_deg 19.511 r_dihedral_angle_3_deg 14.493 r_dihedral_angle_1_deg 5.905 r_scangle_it 2.335 r_scbond_it 1.744 r_mcangle_it 1.668 r_angle_refined_deg 1.278 r_mcbond_it 1.077 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.285 r_symmetry_hbond_refined 0.257 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3654 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction