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DDR1 kinase autoinhibited by its juxtamembrane region
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 9.5 mg/ml protein in 20 mM HEPES pH 7.5, 200 mM NaCl, 1 mM TCEP. Precipitant: 100 mM Tris pH 8.0, 1.5 M ammonium sulphate.
Crystal Properties Matthews coefficient Solvent content 2.78 55.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.307 α = 90 b = 105.307 β = 90 c = 406.939 γ = 120
Symmetry Space Group P 63 2 2
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 2018-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 2.58 58.13 100 0.128 0.979 6.5 20.3 43468 41.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.62 99.1 1.129 0.443 1.2 20.9
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 5bvw 2.58 54.42 1.34 43355 2174 99.86 0.2275 0.2252 0.225 0.2701 0.2692 47.65
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 14.6438 f_angle_d 0.5366 f_chiral_restr 0.039 f_plane_restr 0.0041 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7179 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing