☰ Navigation Tabs
Crystal structure of PKD2 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 11% PEG3350, 0.1 M HEPES, pH 7.5, 0.15 M sodium chloride, 0.003 M magnesium chloride, 0.003 M cadmium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.05 59.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.1 α = 90 b = 79.8 β = 90 c = 111.3 γ = 90
Symmetry Space Group P 21 21 21
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 2009-03-13 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 2.104 19.734 99 0.107 15.29 7.2 31648 -3 24.758
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 2.104 2.2 96.4 0.406 4.85
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 2.104 19.73 31645 1572 98.14 0.1998 0.198 0.2006 0.2359 0.2375 RANDOM 18.6489
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 -0.04 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.611 r_dihedral_angle_4_deg 19.248 r_dihedral_angle_3_deg 14.617 r_dihedral_angle_1_deg 6.254 r_scangle_it 3.931 r_scbond_it 2.413 r_mcangle_it 1.532 r_angle_refined_deg 1.464 r_mcbond_it 0.854 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.611 r_dihedral_angle_4_deg 19.248 r_dihedral_angle_3_deg 14.617 r_dihedral_angle_1_deg 6.254 r_scangle_it 3.931 r_scbond_it 2.413 r_mcangle_it 1.532 r_angle_refined_deg 1.464 r_mcbond_it 0.854 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3137 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 10
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection