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Human MST3 (STK24) kinase in complex with macrocyclic inhibitor JA310
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B32
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein solution: 11 mg/mL MST3 in 25 mM HEPES pH 7.5, 200 mM NaCl, 0.5 mM TCEP, 5% glycerol) with 3 mM macrocyclic inhibitor JA310.
Reservoir solution: 14% PEG 6K, 0.1 M HEPES pH 7.2. Drop ratio 1:2.
Crystal Properties Matthews coefficient Solvent content 2.21 44.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.127 α = 90 b = 79.753 β = 90 c = 100.537 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2022-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.64 42.5 97.7 0.067 0.073 0.998 15.5 6.4 37428 20.7338852028
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.67 97.2 0.719 0.785 0.853 2 6.3
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 1.64 42.5 1.3436046539 37359 1897 97.2460108806 0.181203569395 0.178725536175 0.1833 0.227494078702 0.2299 27.3372861575
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 14.9157834486 f_angle_d 0.823453565445 f_chiral_restr 0.050335928864 f_bond_d 0.00592532859557 f_plane_restr 0.00541872793596
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2188 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing