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Human PDK1 Kinase Domain in Complex with Allosteric Activator PS114 Bound to the PIF-Pocket
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HRC PDB ENTRY 3HRC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 1.2 M NA CITRATE, 0.1 M HEPES PH 7.5, 10 MM DTT.
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.39 α = 90 b = 44.1 β = 100.07 c = 47.3 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 37 94 0.07 13.4 3.8 19306 5.6 21.72
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 2.1 96.5 0.3 5.6 3.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 PDB ENTRY 3HRC 2 36.526 1.39 19306 309 93.59 0.1611 0.1605 0.1587 0.1977 0.2008
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] -0.1938 0.8616 1.9448 -1.751
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.654 f_angle_d 1.095 f_chiral_restr 0.073 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing