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Crystal structure of human Pim-1 kinase in complex with a thiazolamine-indazole inhibitor.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 1.0M LiCl, 0.1M TRIS, 20% PEG6K
Crystal Properties Matthews coefficient Solvent content 3.33 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.291 α = 90 b = 97.291 β = 90 c = 80.489 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 944 2013-12-20 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 2.3 30 99.8 0.091 9.7 7.5 19337
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 2.3 2.38 99.5 0.758 2.98 7.4
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 2.3 29.61 18278 984 99.74 0.18354 0.18155 0.1909 0.22448 0.2317 RANDOM 53.659
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] -1.26 -0.63 -1.26 4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_4_deg 15.714 r_dihedral_angle_3_deg 13.138 r_long_range_B_refined 6.019 r_long_range_B_other 5.954 r_dihedral_angle_1_deg 5.48 r_scangle_other 4.115 r_mcangle_it 3.565 r_mcangle_other 3.564 r_scbond_it 2.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_4_deg 15.714 r_dihedral_angle_3_deg 13.138 r_long_range_B_refined 6.019 r_long_range_B_other 5.954 r_dihedral_angle_1_deg 5.48 r_scangle_other 4.115 r_mcangle_it 3.565 r_mcangle_other 3.564 r_scbond_it 2.507 r_scbond_other 2.507 r_mcbond_it 2.318 r_mcbond_other 2.317 r_angle_refined_deg 1.211 r_angle_other_deg 0.733 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 80 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement MOLREP phasing HKL-2000 data scaling SCALEPACK data scaling HKL-2000 data reduction