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Crystal structure of human Pim-1 kinase in complex with a quinazolinone-pyrrolodihydropyrrolone inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 1.0M LiCl, 0.1M TRIS pH8.0, 20% PEG6K
Crystal Properties Matthews coefficient Solvent content 3.4 63.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.181 α = 90 b = 98.181 β = 90 c = 80.827 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 RIGAKU SATURN 92 2013-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 30 99.8 0.083 8.7 3.4 22588
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 99.6 0.452 2.54 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 29.86 21363 1151 99.81 0.18021 0.17876 0.1845 0.20835 0.2187 RANDOM 37.018
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] 0.1 0.1 0.1 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.019 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_4_deg 12.145 r_dihedral_angle_1_deg 5.103 r_long_range_B_refined 4.938 r_long_range_B_other 4.722 r_scangle_other 2.632 r_mcangle_it 2.57 r_mcangle_other 2.57 r_scbond_it 1.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.019 r_dihedral_angle_3_deg 13.435 r_dihedral_angle_4_deg 12.145 r_dihedral_angle_1_deg 5.103 r_long_range_B_refined 4.938 r_long_range_B_other 4.722 r_scangle_other 2.632 r_mcangle_it 2.57 r_mcangle_other 2.57 r_scbond_it 1.558 r_scbond_other 1.558 r_mcbond_it 1.513 r_mcbond_other 1.512 r_angle_refined_deg 1.026 r_angle_other_deg 0.7 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 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 2225 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing