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Crystal structure of human Pim-1 kinase in complex with an azaspiro pyrazinyl-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 3.37 63.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.815 α = 90 b = 97.815 β = 90 c = 80.585 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 2014-01-24 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 98.4 0.083 11.2 11.4 22333
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 97 0.561 4.95 11.3
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 29.75 20815 1123 98.37 0.1804 0.17891 0.1853 0.20781 0.2091 RANDOM 44.684
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] -1.81 -0.91 -1.81 5.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.05 r_dihedral_angle_4_deg 14.531 r_dihedral_angle_3_deg 12.534 r_long_range_B_refined 5.377 r_long_range_B_other 5.363 r_dihedral_angle_1_deg 5.261 r_scangle_other 3.2 r_mcangle_it 2.902 r_mcangle_other 2.902 r_scbond_it 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.05 r_dihedral_angle_4_deg 14.531 r_dihedral_angle_3_deg 12.534 r_long_range_B_refined 5.377 r_long_range_B_other 5.363 r_dihedral_angle_1_deg 5.261 r_scangle_other 3.2 r_mcangle_it 2.902 r_mcangle_other 2.902 r_scbond_it 1.9 r_scbond_other 1.899 r_mcbond_it 1.807 r_mcbond_other 1.807 r_angle_refined_deg 1.101 r_angle_other_deg 0.718 r_chiral_restr 0.068 r_bond_refined_d 0.007 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 142 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement