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Crystal structure of non-phosphorylated form 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 15% PEG3350, 0.1 M HEPES, 0.2 M sodium chloride, 0.003 M magnesium chloride, 0.003 M cadmium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3 59.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.4 α = 90 b = 79.8 β = 90 c = 110.7 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 2009-04-03 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 1.9 19.95 99 0.092 16.57 8.2 42471 -3 23.945
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 1.9 2 94.6 0.529 2.92
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 1.9 19.95 42471 2133 99.12 0.208 0.207 0.2074 0.2285 0.2279 RANDOM 17.3851
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] -0.2 0.04 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.612 r_dihedral_angle_4_deg 18.997 r_dihedral_angle_3_deg 12.631 r_dihedral_angle_1_deg 5.205 r_scangle_it 2.915 r_scbond_it 1.715 r_mcangle_it 1.147 r_angle_refined_deg 1.072 r_mcbond_it 0.619 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.612 r_dihedral_angle_4_deg 18.997 r_dihedral_angle_3_deg 12.631 r_dihedral_angle_1_deg 5.205 r_scangle_it 2.915 r_scbond_it 1.715 r_mcangle_it 1.147 r_angle_refined_deg 1.072 r_mcbond_it 0.619 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3133 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 15
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection XDS data reduction