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Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a beta carboline ligand I
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 0.14 M Sodium malonate, 0.07 M Bis-Tris-Propane pH 7.5, 14 % PEG 3350, 7 % Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.04 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.371 α = 90 b = 98.371 β = 90 c = 81.332 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 2007-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97912 SLS X10SA
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 2.1 50 100 0.126 0.126 6.3 3.8 26203 26203
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 100 0.724 3.8 2592
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 2.1 36.71 26168 26168 1330 99.95 0.166 0.166 0.164 0.168 0.206 0.209 RANDOM 19.425
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] 0.12 0.06 0.12 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.886 r_dihedral_angle_4_deg 17.488 r_dihedral_angle_3_deg 14.065 r_scangle_it 7.364 r_dihedral_angle_1_deg 6.494 r_scbond_it 5.51 r_mcangle_it 3.4 r_mcbond_it 2.196 r_angle_other_deg 1.653 r_angle_refined_deg 1.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.886 r_dihedral_angle_4_deg 17.488 r_dihedral_angle_3_deg 14.065 r_scangle_it 7.364 r_dihedral_angle_1_deg 6.494 r_scbond_it 5.51 r_mcangle_it 3.4 r_mcbond_it 2.196 r_angle_other_deg 1.653 r_angle_refined_deg 1.477 r_mcbond_other 0.638 r_chiral_restr 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2263 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 26
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