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Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human deubiquitinating enzyme, reveals an unproductive form of the enzyme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 1.6 M Ammonium sulfate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.29 46.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.393 α = 90 b = 41.67 β = 89.93 c = 138.729 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 300 mm CCD mirrors 2008-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03303 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.398 50 99.1 0.084 0.084 14.7 3.5 39644 39644 1.6 1.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.398 2.49 92.1 0.648 0.648 1.6 2.6 3691
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.398 41.7 39644 37595 1987 98.83 0.20403 0.20403 0.20107 0.2077 0.25827 0.259 RANDOM 51.041
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] -0.35 -0.13 0.02 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.407 r_dihedral_angle_4_deg 17.223 r_dihedral_angle_3_deg 15.616 r_angle_other_deg 12.04 r_dihedral_angle_1_deg 4.792 r_scangle_it 4.43 r_mcangle_it 3.277 r_scbond_it 2.579 r_mcbond_it 1.827 r_angle_refined_deg 1.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.407 r_dihedral_angle_4_deg 17.223 r_dihedral_angle_3_deg 15.616 r_angle_other_deg 12.04 r_dihedral_angle_1_deg 4.792 r_scangle_it 4.43 r_mcangle_it 3.277 r_scbond_it 2.579 r_mcbond_it 1.827 r_angle_refined_deg 1.045 r_nbtor_refined 0.302 r_nbtor_other 0.253 r_nbd_refined 0.185 r_nbd_other 0.171 r_symmetry_vdw_refined 0.169 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.111 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7190 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 21
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling