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Crystal structure of DLK with inhibitor bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 15.9% PEG 3350, 0.1M Magnesium Acetate, 0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.02 38.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.429 α = 90 b = 39.775 β = 106.05 c = 62.471 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 100 CCD ADSC QUANTUM 315r 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.98 ALS 5.0.3
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 1.5 47.73 99.9 0.056 0.075 0.049 0.999 12.2 4.1 43736
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.9 1.336 0.326 0.9 3.8
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.5 47.73 43719 2132 99.9 0.206 0.24 0.207 29.34
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] -0.543 -0.052 -0.349 -0.891
RMS Deviations Key Refinement Restraint Deviation OPLS 2005X
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2191 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 37
Software Software Software Name Purpose PRIME-X refinement XDS data reduction Aimless data scaling PHASER phasing