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Staphylococcus aureus serine/threonine kinase Stk1 with inhibitor GW779439X
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EQM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 1 microlitre of 9 mg/mL Stk1 1-291, 5 mM MgCl2, 2% (w/v) benzamidine hydrochloride, 1 mM dithiothreitol, 20 mM HEPES pH 7.5, 150 mM NaCl and 2 mM GW779439X was mixed with 1 microlitre of reservoir solution: 80 mM 2-(N-morpholino)-ethanesulfonic acid, pH 6.0, 1.2 M sodium citrate, pH 7.0, 2% (w/v) benzamidine hydrochloride and 30 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 3.52 65.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.792 α = 90 b = 100.792 β = 90 c = 91.698 γ = 90
Symmetry Space Group P 43 21 2
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 2023-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.0 CLSI 08B1-1
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 2.066 45.08 95.7 0.095 0.093 0.018 1 28.7 25.3 22007 42.62
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 2.066 2.235 80.3 2.01 2.059 0.436 0.643 1.8
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 2.07 45.08 1.34 22005 2000 74.52 0.2162 0.2128 0.2127 0.2495 0.2494 59.23
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 9.7207 f_angle_d 0.5337 f_chiral_restr 0.0429 f_plane_restr 0.005 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2155 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 112
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing