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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 4ALW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Tris, potassium sodium tartrate tetrahydrate
Crystal Properties Matthews coefficient Solvent content 3.57 65.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.672 α = 90 b = 97.672 β = 90 c = 80.579 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 2015-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 42.29 100 14.7 5.2 17210
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 4ALW 2.4 42.29 16362 822 99.98 0.17893 0.17683 0.22273 0.2121 RANDOM 52.909
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] 0.7 0.35 0.7 -2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.036 r_dihedral_angle_4_deg 18.678 r_dihedral_angle_3_deg 15.007 r_dihedral_angle_1_deg 6.742 r_long_range_B_refined 6.436 r_long_range_B_other 6.435 r_scangle_other 5.265 r_mcangle_it 3.972 r_mcangle_other 3.969 r_scbond_it 3.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.036 r_dihedral_angle_4_deg 18.678 r_dihedral_angle_3_deg 15.007 r_dihedral_angle_1_deg 6.742 r_long_range_B_refined 6.436 r_long_range_B_other 6.435 r_scangle_other 5.265 r_mcangle_it 3.972 r_mcangle_other 3.969 r_scbond_it 3.709 r_scbond_other 3.709 r_mcbond_it 2.836 r_mcbond_other 2.835 r_angle_refined_deg 1.993 r_angle_other_deg 0.904 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2130 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing