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Crystal structure of RQA_V phosphopeptide bound to HLA-A2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BH9 PDB ENTRY 3BH9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG8000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.63 53.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.2 α = 90 b = 54.7 β = 104.8 c = 75.2 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU SATURN 944 2007-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5417
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 19.865 98.9 0.053 32.54 10 31595 -3 31.088
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 2.1 96.1 0.465 4.35
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 PDB ENTRY 3BH9 2 19.865 31585 1576 98.95 0.2098 0.2079 0.2094 0.2487 0.2484 RANDOM 26.7458
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] 0.38 -0.91 0.33 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.626 r_dihedral_angle_4_deg 14.004 r_dihedral_angle_3_deg 13.83 r_dihedral_angle_1_deg 5.125 r_scangle_it 3.05 r_scbond_it 1.876 r_mcangle_it 1.259 r_angle_refined_deg 1.171 r_mcbond_it 0.654 r_nbtor_refined 0.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.626 r_dihedral_angle_4_deg 14.004 r_dihedral_angle_3_deg 13.83 r_dihedral_angle_1_deg 5.125 r_scangle_it 3.05 r_scbond_it 1.876 r_mcangle_it 1.259 r_angle_refined_deg 1.171 r_mcbond_it 0.654 r_nbtor_refined 0.289 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.122 r_symmetry_vdw_refined 0.119 r_symmetry_hbond_refined 0.085 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3161 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 13
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection XDS data reduction MOLREP phasing