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Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NB2 PDB ENTRIES 3NB2 AND 1C4Z experimental model PDB 1C4Z PDB ENTRIES 3NB2 AND 1C4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 1.5-1.7 M ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.68 66.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 302.313 α = 90 b = 72.012 β = 109.22 c = 125.669 γ = 90
Symmetry Space Group C 1 2 1
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 mirrors 2009-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97942 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 3.3 50 99 0.138 20.3 4.9 39210 38818 95.13
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) 1 3.3 3.42 95.2 0.635 1.9 4.2 3696
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT PDB ENTRIES 3NB2 AND 1C4Z 3.3 48.08 1.89 38918 38544 1922 99.04 0.2677 0.2662 0.2529 0.2977 0.2932 RANDOM 128.3
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] 34.2366 -36.6552 -30.6654 -3.5712
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.846 f_angle_d 0.87 f_chiral_restr 0.057 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10910 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 63
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling