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Crystal structure of the binary complex between HLA-A2 and HCMV NLV-M5T peptide variant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 9-20% PEG 6000, 0.1M tri-Na Citrate, 0-0.1M NaCl, pH 6.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.095 α = 90 b = 81.036 β = 114.2 c = 57.728 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 CCD MARMOSAIC 225 mm CCD 2008-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 1.8 50 95.4 0.045 0.045 18.2 3.8 46147 31.791
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) 1.8 1.86 87.6 0.38 0.38 3.6 3.8 3415
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 14.94 46147 40283 4192 99.82 0.206 0.206 0.204 0.2055 0.242 RANDOM 28.801
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 32.725 r_dihedral_angle_4_deg 16.285 r_dihedral_angle_3_deg 13.371 r_dihedral_angle_1_deg 5.464 r_scangle_it 2.184 r_scbond_it 1.514 r_angle_refined_deg 1.126 r_mcangle_it 1.118 r_mcbond_it 0.667 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.725 r_dihedral_angle_4_deg 16.285 r_dihedral_angle_3_deg 13.371 r_dihedral_angle_1_deg 5.464 r_scangle_it 2.184 r_scbond_it 1.514 r_angle_refined_deg 1.126 r_mcangle_it 1.118 r_mcbond_it 0.667 r_nbtor_refined 0.293 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.112 r_symmetry_hbond_refined 0.084 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3212 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction