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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 II
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 7 277 0.56 M Na succinate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.06 59.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.668 α = 90 b = 98.668 β = 90 c = 81.129 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 2007-09-14 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 2.01 32.297 100 0.075 0.075 8.4 5.2 29963
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 2.01 2.12 100 0.704 0.704 1.1 5.1 4345
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 2.01 32.297 29927 29927 1553 99.98 0.169 0.169 0.167 0.1679 0.199 0.1971 RANDOM 26.309
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] 0.27 0.13 0.27 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.211 r_dihedral_angle_4_deg 20.209 r_dihedral_angle_3_deg 13.647 r_scangle_it 7.69 r_dihedral_angle_1_deg 6.337 r_scbond_it 5.66 r_mcangle_it 3.382 r_mcbond_it 2.28 r_angle_other_deg 1.609 r_angle_refined_deg 1.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.211 r_dihedral_angle_4_deg 20.209 r_dihedral_angle_3_deg 13.647 r_scangle_it 7.69 r_dihedral_angle_1_deg 6.337 r_scbond_it 5.66 r_mcangle_it 3.382 r_mcbond_it 2.28 r_angle_other_deg 1.609 r_angle_refined_deg 1.371 r_mcbond_other 0.712 r_chiral_restr 0.085 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 2266 Nucleic Acid Atoms Solvent Atoms 207 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