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Human Class I MHC HLA-A2(A150P) in complex with the Tel1p peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TVB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 PEG3350 24%, MES 0.025M, NaF 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.42 49.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.155 α = 90 b = 86.885 β = 89.97 c = 79.409 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 MAR CCD 165 mm 2008-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 20 97.3 0.069 16.54 3.6 57629 56073 1 1 26.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 86.3 0.316 2.52 2.9 4973
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TVB 2 20 57741 56055 2841 97.08 0.174 0.174 0.171 0.1762 0.226 0.2288 RANDOM 36.521
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] -0.62 0.04 1.29 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.213 r_dihedral_angle_4_deg 17.76 r_dihedral_angle_3_deg 16.07 r_dihedral_angle_1_deg 6.504 r_scangle_it 2.402 r_mcangle_it 2.249 r_angle_refined_deg 1.632 r_scbond_it 1.605 r_mcbond_it 1.555 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.213 r_dihedral_angle_4_deg 17.76 r_dihedral_angle_3_deg 16.07 r_dihedral_angle_1_deg 6.504 r_scangle_it 2.402 r_mcangle_it 2.249 r_angle_refined_deg 1.632 r_scbond_it 1.605 r_mcbond_it 1.555 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.255 r_xyhbond_nbd_refined 0.186 r_nbd_refined 0.149 r_chiral_restr 0.12 r_symmetry_vdw_refined 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6338 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction SGX-CAT data collection HKL-2000 data reduction HKL-2000 data scaling