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The ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a 2-glycine linker and crystallized at traditional protein concentration
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QAR 2QAR (for 1TEL), homology model (UBA) experimental model PDB 1TEL 2QAR (for 1TEL), homology model (UBA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 1.2 uL of 15 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 6.50, 750 mM Mg-Formate
Crystal Properties Matthews coefficient Solvent content 2.09 41.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.971 α = 90 b = 67.971 β = 90 c = 55.749 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 2020-12-02 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 2.1 40.48 98.32 0.04076 0.04229 0.01108 1 28.14 14.5 8522 51.29
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 2.1 2.175 96.24 1.088 1.129 0.2973 0.923 2.27 14.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2QAR (for 1TEL), homology model (UBA) 2.1 40.48 1.35 8493 467 98.33 0.2469 0.2452 0.2458 0.2756 0.2773 72.8
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 10.9578 f_angle_d 0.5652 f_chiral_restr 0.0368 f_plane_restr 0.0049 f_bond_d 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1023 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building autoPROC data reduction autoPROC data scaling PHASER phasing