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Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule 2-(4-chlorophenyl)sulfanylacetohydrazide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 HEPES
CaCl2
Glycerol
DTT
BIS-TRIS-propane
PEG3350
Ethylene-glycol
DMSO
Crystal Properties Matthews coefficient Solvent content 3.15 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.315 α = 90 b = 98.315 β = 90 c = 80.504 γ = 120
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 Silicon 2016-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.92 50 99.9 0.086 0.99 15.01 7.99 33834
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 2.04 99.7 0.544 0.91 3.4 8.07
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 3WE8 1.92 41.954 1.37 33828 1692 99.91 0.1595 0.1584 0.1615 0.18 0.1825
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 20.231 f_angle_d 0.75 f_chiral_restr 0.053 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2244 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing