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Crystal structure of the binary complex between HLA-A2 and HCMV NLV-M5Q 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 2.61 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.471 α = 90 b = 81.312 β = 114.33 c = 57.918 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 1.9 50 93.2 0.059 0.059 14.4 3.7 38996 31.648
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) 1.9 1.97 68.5 0.391 0.391 2.4 2.4 2563
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 1.9 14.96 38996 33950 3533 97.8 0.206 0.206 0.205 0.242 RANDOM 30.448
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.317 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_4_deg 14.531 r_dihedral_angle_1_deg 5.788 r_scangle_it 2.461 r_scbond_it 1.661 r_mcangle_it 1.19 r_angle_refined_deg 1.176 r_mcbond_it 0.726 r_nbtor_refined 0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.317 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_4_deg 14.531 r_dihedral_angle_1_deg 5.788 r_scangle_it 2.461 r_scbond_it 1.661 r_mcangle_it 1.19 r_angle_refined_deg 1.176 r_mcbond_it 0.726 r_nbtor_refined 0.291 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.194 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3193 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