☰ Navigation Tabs
Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HD5 PDB entry 2HD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 277 0.2M ammonium citrate, 18% PEG 3,350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.54 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.424 α = 90 b = 103.519 β = 108.09 c = 70.35 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 315 2009-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 50 93.9 0.092 35.3 9.2 22908 22908 50
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 64.4 0.304 3.1 4.5 1569
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD+MR PDB entry 2HD5 2.7 48.116 0.09 22908 2073 88.81 0.237 0.234 0.2297 0.3 0.297 75.484
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] 27.635 -13.829 -6.489 -21.146
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.279 f_angle_d 1.064 f_chiral_restr 0.074 f_bond_d 0.009 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5509 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection PHENIX phasing