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Structure of the Catalytic Domain of Human Ubiquitin Carboxyl-terminal Hydrolase 8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 298 18% PEG3350; 0.1 M bis-Tris, pH 6.3, 0.2 M KSCN, 1 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 298, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.77 55.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.173 α = 90 b = 67.173 β = 90 c = 194.458 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 CCD SBC-3 2006-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97896 APS 19-BM
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 18.2 99.4 0.085 20.03 5.4 33281 33281 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2 18.2 33136 31452 1684 99.31 0.17056 0.16845 0.1709 0.21023 0.2078 RANDOM 39.287
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] 1.12 0.56 1.12 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.312 r_dihedral_angle_4_deg 19.789 r_dihedral_angle_3_deg 15.072 r_scangle_it 6.218 r_dihedral_angle_1_deg 5.855 r_scbond_it 4.711 r_mcangle_it 3.078 r_mcbond_it 2.245 r_angle_refined_deg 1.498 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.312 r_dihedral_angle_4_deg 19.789 r_dihedral_angle_3_deg 15.072 r_scangle_it 6.218 r_dihedral_angle_1_deg 5.855 r_scbond_it 4.711 r_mcangle_it 3.078 r_mcbond_it 2.245 r_angle_refined_deg 1.498 r_nbtor_refined 0.31 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.153 r_symmetry_vdw_refined 0.127 r_chiral_restr 0.111 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2746 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing