☰ Navigation Tabs
Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a pyrrolo[2,3-a]carbazole ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C3I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2M NaNO3 0.1M
BTProp pH 8.5
20% PEG3350
10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.821 α = 90 b = 97.821 β = 90 c = 80.743 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 2008-07-07 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 2.35 23.577 99.9 0.127 0.127 10.6 4.6 18404 18386 43.4
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 2.35 2.48 100 0.763 0.763 2 4.6 2654
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 2C3I 2.35 23.577 18363 18359 913 99.98 0.176 0.176 0.173 0.1842 0.226 0.2362 RANDOM 19.441
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] 0.58 0.29 0.58 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.384 r_dihedral_angle_4_deg 14.338 r_dihedral_angle_3_deg 13.779 r_scangle_it 10.075 r_scbond_it 8.9 r_dihedral_angle_1_deg 6.044 r_mcangle_it 5.274 r_mcbond_it 3.779 r_angle_refined_deg 1.549 r_mcbond_other 1.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.384 r_dihedral_angle_4_deg 14.338 r_dihedral_angle_3_deg 13.779 r_scangle_it 10.075 r_scbond_it 8.9 r_dihedral_angle_1_deg 6.044 r_mcangle_it 5.274 r_mcbond_it 3.779 r_angle_refined_deg 1.549 r_mcbond_other 1.223 r_angle_other_deg 0.914 r_chiral_restr 0.088 r_bond_refined_d 0.016 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 2267 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 18
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction