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Human PIM1 bound to benzothiophene inhibitor 213
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 25% PEG3350, 0.1 M TRIS pH8.5, 0.2 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.92 57.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.921 α = 90 b = 96.921 β = 90 c = 80.092 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 PIXEL DECTRIS PILATUS3 S 6M 2019-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 31.72 99.9 0.109 0.111 0.025 1 23.3 20.4 21801
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.9 2.465 2.526 0.553 0.828 20.6
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 4IJP 2.2 31.72 20653 1118 99.93 0.1768 0.1742 0.182 0.226 0.2293 RANDOM 57.839
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] 1.84 0.92 1.84 -5.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.001 r_dihedral_angle_4_deg 16.867 r_dihedral_angle_3_deg 14.905 r_dihedral_angle_1_deg 6.846 r_angle_refined_deg 1.512 r_angle_other_deg 1.303 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.001 r_dihedral_angle_4_deg 16.867 r_dihedral_angle_3_deg 14.905 r_dihedral_angle_1_deg 6.846 r_angle_refined_deg 1.512 r_angle_other_deg 1.303 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2274 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing