☰ Navigation Tabs
Crystal structure of Pim1 kinase in complex with inhibitor (Z)-2-[(1H-indol-3-yl)methylene]-7-(azepan-1-ylmethyl)-6-hydroxybenzofuran-3(2H)-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A99
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 100mM Citrate buffer pH 5.5, 200mM NaCl, 1M NH4HPO4, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.29 62.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.214 α = 90 b = 98.214 β = 90 c = 80.881 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 RAYONIX MX225HE 2009-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.55 85.13 99.4 0.074 0.074 8.3 5.8 14489 14489 54.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.69 98.9 0.404 0.404 0.445 0.184 1.9 5.8 2099
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 3A99 2.55 85.126 14485 714 99.43 0.1798 0.1773 0.1742 0.2288 0.2228 RANDOM 38.2663
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] 0.92 0.46 0.92 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.036 r_dihedral_angle_4_deg 19.079 r_dihedral_angle_3_deg 15.975 r_dihedral_angle_1_deg 6.432 r_scangle_it 5.066 r_scbond_it 3.032 r_mcangle_it 2.073 r_angle_refined_deg 1.993 r_mcbond_it 1.07 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.036 r_dihedral_angle_4_deg 19.079 r_dihedral_angle_3_deg 15.975 r_dihedral_angle_1_deg 6.432 r_scangle_it 5.066 r_scbond_it 3.032 r_mcangle_it 2.073 r_angle_refined_deg 1.993 r_mcbond_it 1.07 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2099 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 34
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOSFLM data reduction