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Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M Hepes pH 6.5,
10% (w/v) PEG 8000,
20% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.6 α = 90 b = 102.084 β = 90 c = 120.903 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 MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors with two additional horizontally deflecting mirrors 2010-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.94944 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 1.89 35.1 99.8 0.096 0.096 29.5 13.7 78011 73928 2 2
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) 1.89 1.93 98.8 0.886 0.886 2.25 8.4
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 1.89 35.1 73928 3934 99.26 0.16148 0.15904 0.169 0.20757 0.2149 RANDOM 30.086
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] 0.48 0.18 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.263 r_dihedral_angle_4_deg 16.456 r_dihedral_angle_3_deg 14.993 r_dihedral_angle_1_deg 5.499 r_scangle_it 5.245 r_scbond_it 3.792 r_mcangle_it 2.293 r_angle_refined_deg 1.399 r_mcbond_it 1.347 r_angle_other_deg 0.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.263 r_dihedral_angle_4_deg 16.456 r_dihedral_angle_3_deg 14.993 r_dihedral_angle_1_deg 5.499 r_scangle_it 5.245 r_scbond_it 3.792 r_mcangle_it 2.293 r_angle_refined_deg 1.399 r_mcbond_it 1.347 r_angle_other_deg 0.859 r_mcbond_other 0.428 r_chiral_restr 0.18 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6391 Nucleic Acid Atoms Solvent Atoms 845 Heterogen Atoms 18
Software Software Software Name Purpose Blu-Ice data collection SHELXD phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling