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Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule (E)-4-(4-hydroxyphenyl)but-3-en-2-one
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
LiCl
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 = 98.553 α = 90 b = 98.553 β = 90 c = 80.941 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 CCD MARMOSAIC 225 mm CCD 2016-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
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 2.257 50 97.1 0.078 0.99 13.43 3.17 20497
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 2.257 2.39 97.1 0.613 0.75 2.23 3.26
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 2.257 37.749 1.36 20493 1025 97.08 0.1804 0.1789 0.1821 0.2077 0.2117
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 21.902 f_angle_d 0.787 f_chiral_restr 0.051 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2226 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing