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Human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and Leucettine L41
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 0.16M Na(OAc), 0.08M BTProp pH 8.5 , 16% PEG3350, 8% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3 59.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.006 α = 90 b = 98.006 β = 90 c = 80.497 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 2008-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 19.582 97 0.074 0.074 17.7 6.3 29755 28862 34.5
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 2.11 94.9 0.91 0.91 0.9 6.2 4114
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 19.58 29708 28852 1456 97.12 0.1776 0.1776 0.1758 0.1832 0.213 0.2159 RANDOM 36.226
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] 0.98 0.49 0.98 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.563 r_dihedral_angle_4_deg 15.592 r_dihedral_angle_3_deg 14.219 r_scangle_it 9.303 r_scbond_it 7.728 r_dihedral_angle_1_deg 5.918 r_mcangle_it 4.531 r_mcbond_it 3.392 r_angle_refined_deg 1.515 r_mcbond_other 1.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.563 r_dihedral_angle_4_deg 15.592 r_dihedral_angle_3_deg 14.219 r_scangle_it 9.303 r_scbond_it 7.728 r_dihedral_angle_1_deg 5.918 r_mcangle_it 4.531 r_mcbond_it 3.392 r_angle_refined_deg 1.515 r_mcbond_other 1.145 r_angle_other_deg 0.935 r_chiral_restr 0.098 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 2284 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 27
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction