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Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and the JNK inhibitor V
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 7.5 277 9 % PEG 10000, 7.2 % Ethylene glycol, 0.09 M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.01 59.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.239 α = 90 b = 98.239 β = 90 c = 80.723 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 2007-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 2.15 31.189 100 0.103 0.103 7.2 4.9 24190
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) 1 2.15 2.27 100 0.747 0.747 1 4.8 3511
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2C3I 2.15 31.189 24159 24159 1208 99.95 0.165 0.165 0.163 0.205 0.2093 RANDOM 28.525
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] 0.18 0.09 0.18 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.524 r_dihedral_angle_4_deg 15.981 r_dihedral_angle_3_deg 12.729 r_scangle_it 7.909 r_scbond_it 6.267 r_dihedral_angle_1_deg 6.15 r_mcangle_it 3.672 r_mcbond_it 2.506 r_angle_refined_deg 1.464 r_angle_other_deg 1.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.524 r_dihedral_angle_4_deg 15.981 r_dihedral_angle_3_deg 12.729 r_scangle_it 7.909 r_scbond_it 6.267 r_dihedral_angle_1_deg 6.15 r_mcangle_it 3.672 r_mcbond_it 2.506 r_angle_refined_deg 1.464 r_angle_other_deg 1.001 r_mcbond_other 0.788 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2260 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 31
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction