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Crystal structure of PDGFRA in Complex with WQ-C-159
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M KCl, 20% PEG 3350, pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.61 23.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.776 α = 90 b = 49.372 β = 90 c = 108.696 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 PIXEL DECTRIS PILATUS3 6M 2016-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 50 96.8 41.6 12.2 26385
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5K5X 1.77 44.952 1.37 26303 1335 99.83 0.1581 0.157 0.1599 0.1793 0.1798
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.016 f_angle_d 1.381 f_chiral_restr 0.087 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2252 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 47
Software Software Software Name Purpose PHENIX refinement DENZO data reduction HKL-3000 data scaling PHASER phasing