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Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QYU PDB ENTRIES 2QYU AND 1C4Z experimental model PDB 1C4Z PDB ENTRIES 2QYU AND 1C4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M MES, 1.6 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.04 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.12 α = 90 b = 118.363 β = 90 c = 241.671 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 2008-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03324 APS 23-ID-D
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 3.2 50 86.7 0.147 7.19 3.1 31621 31621 85.18
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 3.2 3.31 83.7 0.52 0.52 2.39 2.7 3105
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT PDB ENTRIES 2QYU AND 1C4Z 3.27 45.424 1.34 31621 31609 1571 93.76 0.2144 0.2112 0.2054 0.2746 0.2674 RANDOM
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] 1.5143 -3.8234 2.309
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.767 f_angle_d 0.864 f_chiral_restr 0.059 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11640 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 5
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling