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The ubiquitin-associated domain of human thirty-eight negative kinase 1, fused to the 2TEL crystallization chaperone via a 2-glycine linker
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TCY experimental model PDB 7TDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 100mM BisTris, pH 6.0, 960mM Mg-formate
Crystal Properties Matthews coefficient Solvent content 2.83 56.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.725 α = 90 b = 105.725 β = 90 c = 50.917 γ = 120
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 PILATUS 6M Rh coated collimating mirror, K-B focusing mirrors 2023-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 2.4 45.78 99.12 0.1028 0.1083 0.03386 0.999 10.88 10.2 12862 68.73
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 2.4 2.4 92 3.597 3.786 1.173 0.449 0.62 10.2
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 2.4 45.78 1.34 12783 713 98.89 0.2313 0.2294 0.2295 0.2634 0.2626 82.94
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 10.77 f_angle_d 0.4801 f_chiral_restr 0.0369 f_plane_restr 0.0041 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1775 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement Coot model building autoPROC data reduction autoPROC data scaling PHASER phasing