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Pim1 in complex with 4-(4-hydroxyphenethyl)benzoic acid and Pimtide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291.15 100 mM bis-tris-propane (pH 7.0), 10% ethylene glycol, 0.3% DMSO, 20% PEG3350, 200 mM Mg(OAc)2
Crystal Properties Matthews coefficient Solvent content 3.1 59.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.115 α = 90 b = 97.115 β = 90 c = 79.938 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 PILATUS 6M 2021-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.21 48.56 99.6 0.99 28.1 11.3 21576 35.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.22 0.95
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.21 36.1 1.38 21568 1078 99.6 0.1628 0.1613 0.1615 0.1919 0.1921 39.89
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.0937 f_angle_d 0.7729 f_chiral_restr 0.0518 f_plane_restr 0.0082 f_bond_d 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2217 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 18
Software Software Software Name Purpose MxCuBE data collection PHENIX refinement XDS data reduction XDS data scaling PHASER phasing Coot model building