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Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 27% PEG3350, 0.2 M Li2SO4, 0.1 M bisTris, pH 5.6, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298 K
Crystal Properties Matthews coefficient Solvent content 2.68 53.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.682 α = 90 b = 64.82 β = 90 c = 151.895 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 SBC-3 2005-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97883 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 2.1 33.81 90.5 0.094 16.6 6.5 18987 18987 -3
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) 2.1 2.18 80.2 0.444 3.15 6.2 16
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 2.1 33.81 18934 17952 976 90.56 0.21091 0.20829 0.2103 0.25943 0.2599 RANDOM 31.08
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] 1.21 -0.89 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.527 r_dihedral_angle_4_deg 20.382 r_dihedral_angle_3_deg 17.298 r_scangle_it 7.389 r_scbond_it 4.841 r_dihedral_angle_1_deg 4.6 r_mcangle_it 3.239 r_mcbond_it 2.211 r_angle_refined_deg 1.342 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.527 r_dihedral_angle_4_deg 20.382 r_dihedral_angle_3_deg 17.298 r_scangle_it 7.389 r_scbond_it 4.841 r_dihedral_angle_1_deg 4.6 r_mcangle_it 3.239 r_mcbond_it 2.211 r_angle_refined_deg 1.342 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2186 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing