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Human Pim-1 kinase in complex with an inhibitor identified by virtual screening
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 6.3 277 0.1 M imidazole pH 6.3
1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 3.02 59.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.645 α = 90 b = 98.645 β = 90 c = 80.699 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 PIXEL DECTRIS PILATUS 6M 2015-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9762 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.86 19.61 98.3 0.065 0.071 0.026 0.996 14.9 6.7 36740
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.862 1.894 99.8 0.585 0.638 0.248 0.853 2.2 6
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 3R04 1.86 19.61 34889 1851 98.12 0.1602 0.1584 0.1702 0.1942 0.1975 RANDOM 43.51
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] 0.71 0.36 0.71 -2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.185 r_dihedral_angle_4_deg 21.841 r_dihedral_angle_3_deg 13.757 r_dihedral_angle_1_deg 6.556 r_angle_refined_deg 1.734 r_angle_other_deg 1.454 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.185 r_dihedral_angle_4_deg 21.841 r_dihedral_angle_3_deg 13.757 r_dihedral_angle_1_deg 6.556 r_angle_refined_deg 1.734 r_angle_other_deg 1.454 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2268 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling