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Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.28 62.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.329 α = 90 b = 110.933 β = 109.46 c = 73.016 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 PIXEL DECTRIS EIGER X 16M 2023-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9793 SSRF BL02U1
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 2.17 68.84 91.8 0.074 0.089 0.048 0.997 1.5 3.3 30286
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 2.17 2.35 52.9 0.798 0.977 0.557 0.507 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.17 58.5 30267 91.8 0.1988 0.202 0.2342 0.2357
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4262 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 59
Software Software Software Name Purpose Aimless data scaling PHENIX refinement autoPROC data reduction MOLREP phasing