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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 very low protein concentration
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QAR 2QAR, 7TCY experimental model PDB 7TCY 2QAR, 7TCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 1.2 uL of 0.5 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 6.00, 630-750 mM Mg-Formate.
Crystal Properties Matthews coefficient Solvent content 2.04 39.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.375 α = 90 b = 67.375 β = 90 c = 58.683 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 2021-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 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 2.03 33.69 89.42 0.2204 0.2264 0.05108 0.998 11.07 19.5 8862 27.16
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 2.03 2.103 100 1.842 1.89 0.4189 0.839 2.39 20.2
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, 7TCY 2.03 33.69 1.35 8862 433 89.48 0.2034 0.2019 0.2014 0.2318 0.2303 33.07
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 12.4918 f_angle_d 0.6223 f_chiral_restr 0.0378 f_plane_restr 0.0072 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1189 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 1
Software Software Software Name Purpose Coot model building PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing