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Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 0.1 M Na Citrate (5.2),
16% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.577 α = 90 b = 103.986 β = 90 c = 106.076 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 RIGAKU SATURN 944+ VariMax 2010-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.45 50 98.5 0.114 0.114 14.4 6.3 34045 32191 2 2
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 MOLECULAR REPLACEMENT THROUGHOUT 2.45 50 32191 1715 97.82 0.20525 0.20166 0.194 0.27296 0.2633 RANDOM 29.217
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] 0.01 -1.41 1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.266 r_dihedral_angle_4_deg 17.13 r_dihedral_angle_3_deg 15.621 r_dihedral_angle_1_deg 4.94 r_scangle_it 4.71 r_scbond_it 3.268 r_mcangle_it 2.095 r_mcbond_it 1.158 r_angle_refined_deg 0.974 r_angle_other_deg 0.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.266 r_dihedral_angle_4_deg 17.13 r_dihedral_angle_3_deg 15.621 r_dihedral_angle_1_deg 4.94 r_scangle_it 4.71 r_scbond_it 3.268 r_mcangle_it 2.095 r_mcbond_it 1.158 r_angle_refined_deg 0.974 r_angle_other_deg 0.671 r_mcbond_other 0.266 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_gen_planes_other 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 5682 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 7
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling