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Crystal structure of the Lys29, Lys33-linkage-specific TRABID OTU deubiquitinase domain reveals an Ankyrin-repeat ubiquitin binding domain (AnkUBD)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.9 150 MM NACL, 100 MM NAOAC, 5 MM MGCL2, 50 MM MES [PH 5.9]
Crystal Properties Matthews coefficient Solvent content 2.77 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.4 α = 90 b = 72.15 β = 90 c = 133.01 γ = 90
Symmetry Space Group P 21 21 21
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 2008-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.23 46.32 100 0.08 12.1 4.1 29095 2 34.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.35 100 0.49 2.7 4.1
Refinement Statistics Diffraction ID Structure Solution 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 SIRAS NONE 2.23 44.712 0.8 54669 3741 99.95 0.2035 0.2001 0.1932 0.2478 0.2421
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 18.102 f_angle_d 1.413 f_chiral_restr 0.099 f_bond_d 0.013 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3411 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling SHARP phasing