☰ Navigation Tabs
Crystal structure of Pim1 kinase in complex with small molecule inhibitor
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 3.21 61.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.006 α = 90 b = 97.006 β = 90 c = 80.898 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 2009-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.0 SPring-8 BL32B2
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 2.2 29.14 100 0.083 0.083 33.8 22.8 22062 34.61
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 2.2 2.32 100 0.427 0.427 0.437 0.091 1.8 22.7 3189
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3A99 2.2 29.14 20930 1102 99.99 0.1682 0.1664 0.2011 0.193 RANDOM 30.7977
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] 0.86 0.43 0.86 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.174 r_dihedral_angle_4_deg 16.469 r_dihedral_angle_3_deg 13.041 r_dihedral_angle_1_deg 5.666 r_scangle_it 3.917 r_scbond_it 2.406 r_mcangle_it 1.661 r_angle_refined_deg 1.294 r_mcbond_it 0.861 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.174 r_dihedral_angle_4_deg 16.469 r_dihedral_angle_3_deg 13.041 r_dihedral_angle_1_deg 5.666 r_scangle_it 3.917 r_scbond_it 2.406 r_mcangle_it 1.661 r_angle_refined_deg 1.294 r_mcbond_it 0.861 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2168 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 36
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction