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Crystal Structure of Pim-1 Kinase in complex with inhibitor (2E,5Z)-2-(2-chlorophenylimino)-5-(4-hydroxy-3-nitrobenzylidene)thiazolidin-4-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 100mM Citrate buffer, pH 5.5, 200mM NaCl, 1M NH4HPO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.22 61.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.074 α = 90 b = 97.074 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 IMAGE PLATE RIGAKU RAXIS IV++ 2009-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.8 31.782 99.9 0.086 0.086 40.1 22.7 10791 10791 60.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 100 0.385 0.385 0.394 0.082 2 22.6 1565
Refinement Statistics Diffraction ID Structure Solution 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 3UMX 2.8 31.775 1.36 10762 544 99.93 0.1923 0.1902 0.1873 0.2326 0.2249 43.2285
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] 2.6182 2.6182 -5.2364
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.147 f_angle_d 0.891 f_chiral_restr 0.058 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2160 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 30
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction CrystalClear data collection