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Crystal structure of Ser/Thr kinase Pim1 in complex with 10-DEBC derivatives
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YWV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 0.4M potassium sodium tartrate tetrahydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.58 65.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.031 α = 90 b = 98.031 β = 90 c = 80.915 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 291 IMAGE PLATE RIGAKU RAXIS IV++ 2018-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 0.97918
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.1 84.9 97.7 0.997 25.7 11.3 25250
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.101 2.156 0.888 0.874
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1YWV 2.1 84.9 24033 1217 97.72 0.1989 0.1979 0.2058 0.2176 0.219 RANDOM 41.657
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.549 r_dihedral_angle_4_deg 20.828 r_dihedral_angle_3_deg 15.492 r_dihedral_angle_1_deg 5.824 r_angle_other_deg 3.622 r_angle_refined_deg 1.395 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_other 0.007 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.549 r_dihedral_angle_4_deg 20.828 r_dihedral_angle_3_deg 15.492 r_dihedral_angle_1_deg 5.824 r_angle_other_deg 3.622 r_angle_refined_deg 1.395 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2197 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling PHASES phasing