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Crystal structure of the binary complex between HLA-A2 and HCMV NLV-M5S 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 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.047 α = 90 b = 80.897 β = 114.17 c = 57.659 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 ADSC QUANTUM 4 2008-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.12 50 93.4 0.042 0.042 27.71 3.6 27129 29.46
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) 2.12 2.19 69.7 0.169 0.169 6.7 2.4 1656
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.12 14.92 27129 24142 2487 95.93 0.199 0.199 0.196 0.246 RANDOM 35.564
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] -0.02 -0.06 0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.144 r_dihedral_angle_4_deg 16.096 r_dihedral_angle_3_deg 15.583 r_dihedral_angle_1_deg 6.261 r_scangle_it 2.499 r_scbond_it 1.67 r_angle_refined_deg 1.232 r_mcangle_it 1.165 r_mcbond_it 0.692 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.144 r_dihedral_angle_4_deg 16.096 r_dihedral_angle_3_deg 15.583 r_dihedral_angle_1_deg 6.261 r_scangle_it 2.499 r_scbond_it 1.67 r_angle_refined_deg 1.232 r_mcangle_it 1.165 r_mcbond_it 0.692 r_nbtor_refined 0.293 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3202 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction