☰ Navigation Tabs
Crystal structure of sugar aminotransferase WecE from Escherichia coli K-12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MDO ensemble model of 1MDO, 3DR7, 3FRK, 4LC3 and 4OCA experimental model PDB 3DR7 ensemble model of 1MDO, 3DR7, 3FRK, 4LC3 and 4OCA experimental model PDB 3FRK ensemble model of 1MDO, 3DR7, 3FRK, 4LC3 and 4OCA experimental model PDB 4LC3 ensemble model of 1MDO, 3DR7, 3FRK, 4LC3 and 4OCA experimental model PDB 4OCA ensemble model of 1MDO, 3DR7, 3FRK, 4LC3 and 4OCA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Protein solution (10~25 mg/ml, 25 mM Tris or HEPES pH 7.5, 150 mM NaCl) mixed in a 1:1 ratio with the well solution (0.1 M Sodium Acetate, 0.1 M MES pH6.5, 30% (w/v) PEG 2000 MME), cryoprotected with 27% PEG 2000 MME and 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.341 α = 90 b = 87.483 β = 91.1 c = 161.554 γ = 90
Symmetry Space Group P 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 225 mm CCD 2004-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.979 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 48.8 84.23 0.1109 10.31 3 275071 90907
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 MOLECULAR REPLACEMENT FREE R-VALUE ensemble model of 1MDO, 3DR7, 3FRK, 4LC3 and 4OCA 2.7 48.801 0.25 86559 1709 89.77 0.2372 0.2363 0.237 0.2754 0.2718 41.2807
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.445 f_angle_d 0.503 f_chiral_restr 0.02 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22629 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX phasing PDB_EXTRACT data extraction PHENIX refinement XSCALE data scaling