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Crystal structure of Ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from Saccharomyces cerevisiae at 1.74 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 277 16% PEG MME 2000, 0.03M Tris_base, 0.07M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K 2 VAPOR DIFFUSION,SITTING DROP,NANODROP 277 21% PEG MME 2000, 0.03M Tris_base, 0.07M Tris Cl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 42.44 2.29 45.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.231 α = 90 b = 79.449 β = 90 c = 106.339 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 ADSC 2003-07-25 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD APS water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2003-07-17 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1 2 SYNCHROTRON APS BEAMLINE 19-BM 0.96112, 0.97963,0.97946 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 1.74 79.45 98.2 0.052 15.3 4 42823 36.27
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 1.74 1.79 89.8 0.594 2.1 2.8 2820
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 1.74 63.65 40625 2129 99.02 0.18069 0.17917 0.187 0.20892 0.2144 RANDOM 21.059
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] -2.92 0.32 2.59
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.49 r_dihedral_angle_1_deg 5.866 r_scbond_it 5.018 r_mcangle_it 3.126 r_mcbond_it 1.889 r_angle_refined_deg 1.304 r_angle_other_deg 0.767 r_symmetry_vdw_other 0.294 r_nbd_other 0.238 r_nbd_refined 0.201
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.49 r_dihedral_angle_1_deg 5.866 r_scbond_it 5.018 r_mcangle_it 3.126 r_mcbond_it 1.889 r_angle_refined_deg 1.304 r_angle_other_deg 0.767 r_symmetry_vdw_other 0.294 r_nbd_other 0.238 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.086 r_nbtor_other 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2964 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SHELXD phasing autoSHARP phasing SOLOMON phasing REFMAC refinement CCP4 data scaling