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Serine/threonine-protein kinase 40 (STK40) kinase homology domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100mM Tris-HCL 7.5
21% PEG 4000
6% Glycerol
5% Tert-butanol
200mM NaCl
1mM TCEP 2 VAPOR DIFFUSION, HANGING DROP 7.5 293 100mM Tris-HCL 7.5
18% PEG 4000
9% Tert-butanol
75mM NaCl
1mM TCEP
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.55 α = 90 b = 237.65 β = 106.32 c = 55.61 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 6M 2016-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.53 59.41 98.6 0.06 0.99 12.52 3.4 45250
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.53 2.62 99 0.78 0.6 1.49 3.5
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 2VZ6 2.53 59.413 40.16 45250 2407 98.59 0.2587 0.2576 0.2691 0.2795 0.2907
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 7.807 f_angle_d 0.632 f_chiral_restr 0.043 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8279 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing