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The ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a GSGG linker
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 1.2 uL of 1 mg/mL protein in 50 mM Tris pH 8.8, 200 mM KCl combined with 1.2 uL of 100 mM Bis-tris-propane, 2.5 M Ammonium Nitrate
Crystal Properties Matthews coefficient Solvent content 2.16 43.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.651 α = 90 b = 68.651 β = 90 c = 56.735 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 Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1 2021-06-29 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 1.89 34.33 99.92 0.06456 0.06703 0.0179 0.999 20.93 14 12236 39.92
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 1.89 1.959 100 1.631 0.99 0.4415 0.903 2.59 14.6
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 7TCY 1.89 34.33 1.36 12228 595 99.93 0.2243 0.2238 0.2238 0.2347 0.2314 56.32
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 9.8708 f_angle_d 0.5444 f_chiral_restr 0.0365 f_plane_restr 0.0036 f_bond_d 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1095 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement PHASER phasing autoPROC data scaling PHASER phasing Coot model building autoPROC data processing