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Crystal Structure of the human PIM1 kinase domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 Na2SO4, Bis-Tris propane, PEG3350, Ethylene Glycol, DMSO, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.7 66.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.55 α = 90 b = 99.55 β = 90 c = 80.06 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 IMAGE PLATE RIGAKU RAXIS HTC Multi-layer VariMax HR 2004-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 86.07 99.5 0.068 0.068 18.4 6.3 41697 41578 30.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 98.2 0.781 0.781 1.5 4.1 5939
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.8 58.67 47251 39589 2136 58.67 0.18164 0.18164 0.17999 0.1787 0.21336 0.2132 RANDOM 36.881
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.6 r_dihedral_angle_4_deg 18.091 r_dihedral_angle_3_deg 13.182 r_dihedral_angle_1_deg 5.769 r_scangle_it 4.094 r_scbond_it 2.586 r_angle_refined_deg 1.914 r_mcangle_it 1.648 r_mcbond_it 1.026 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.6 r_dihedral_angle_4_deg 18.091 r_dihedral_angle_3_deg 13.182 r_dihedral_angle_1_deg 5.769 r_scangle_it 4.094 r_scbond_it 2.586 r_angle_refined_deg 1.914 r_mcangle_it 1.648 r_mcbond_it 1.026 r_nbtor_refined 0.306 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.112 r_symmetry_vdw_refined 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2213 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling PHASER phasing