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Crystal structure of Pim1 kinase in complex with inhibitor (Z)-2-[(1H-indazol-3-yl)methylene]-6-methoxy-7-(piperazin-1-ylmethyl)benzofuran-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 62.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.28 α = 90 b = 98.28 β = 90 c = 80.641 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 MX-225 2011-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0 SPring-8 BL26B2
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 2.08 32.174 99.7 0.078 0.078 6 6.4 26602 26602 29.1
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 2.08 2.19 100 0.391 0.391 0.425 0.166 2 6.4 3888
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 2.08 32.17 26602 1346 99.77 0.1749 0.1735 0.174 0.2003 0.1995 RANDOM 30.2034
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] 0.63 0.32 0.63 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.036 r_dihedral_angle_4_deg 16.623 r_dihedral_angle_3_deg 13.182 r_dihedral_angle_1_deg 5.5 r_scangle_it 3.679 r_scbond_it 2.226 r_mcangle_it 1.591 r_angle_refined_deg 1.506 r_mcbond_it 0.828 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.036 r_dihedral_angle_4_deg 16.623 r_dihedral_angle_3_deg 13.182 r_dihedral_angle_1_deg 5.5 r_scangle_it 3.679 r_scbond_it 2.226 r_mcangle_it 1.591 r_angle_refined_deg 1.506 r_mcbond_it 0.828 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2131 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 40
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOSFLM data reduction