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Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a furan-thiazolidinedione ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C3I pdb entry 2C3I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M BTP, 20 % PEG 3350 10 % ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.99 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.843 α = 90 b = 97.843 β = 90 c = 80.428 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 HTC 2009-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5
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 2.2 37.484 100 0.101 0.101 13.3 5.6 22340 22340 39.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.32 100 0.851 0.851 0.9 5.5 3251
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2C3I 2.2 37.48 22314 22310 1110 99.98 0.1878 0.1878 0.1858 0.1793 0.2268 0.2173 RANDOM 40.7836
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] 0.92 0.46 0.92 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.699 r_dihedral_angle_4_deg 15.974 r_dihedral_angle_3_deg 14.62 r_scangle_it 9.961 r_scbond_it 8.489 r_dihedral_angle_1_deg 6.102 r_mcangle_it 5.243 r_mcbond_it 3.586 r_angle_refined_deg 1.569 r_mcbond_other 1.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.699 r_dihedral_angle_4_deg 15.974 r_dihedral_angle_3_deg 14.62 r_scangle_it 9.961 r_scbond_it 8.489 r_dihedral_angle_1_deg 6.102 r_mcangle_it 5.243 r_mcbond_it 3.586 r_angle_refined_deg 1.569 r_mcbond_other 1.165 r_angle_other_deg 0.938 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2270 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 28
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction