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Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a naphtho-difuran 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 8.5 277 20% Isopropanol
0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.03 59.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.707 α = 90 b = 97.707 β = 90 c = 80.581 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 2008-03-10 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 2.3 36.37 97.7 0.079 0.076 8.6 3.8 19531 19082
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) 2.3 2.38 100 0.446 0.446 2.1 3.8 1950
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 2.3 36.37 19492 19034 942 97.65 0.172 0.172 0.169 0.1734 0.233 0.2355 RANDOM 43.092
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] 1.91 0.95 1.91 -2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_3_deg 15.273 r_dihedral_angle_4_deg 13.908 r_scangle_it 11.261 r_scbond_it 9.264 r_mcangle_it 5.883 r_dihedral_angle_1_deg 5.812 r_mcbond_it 3.955 r_angle_refined_deg 1.641 r_mcbond_other 1.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_3_deg 15.273 r_dihedral_angle_4_deg 13.908 r_scangle_it 11.261 r_scbond_it 9.264 r_mcangle_it 5.883 r_dihedral_angle_1_deg 5.812 r_mcbond_it 3.955 r_angle_refined_deg 1.641 r_mcbond_other 1.227 r_angle_other_deg 0.957 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2216 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 22
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling