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Crystal structure of GlucDRP from E. coli K-12 MG1655 (EFI target EFI-506058)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 282 Protein solution was at 20 mg/mL containing 50 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME. Mother liqueur contained 0.2 M Na citrate (pH 4.6), 20% PEG 3,350. 20% glycerol was used as the cryoprotectant, vapor diffusion, hanging drop, temperature 282K
Crystal Properties Matthews coefficient Solvent content 2.96 58.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.09 α = 101.47 b = 94.03 β = 96.74 c = 155.2 γ = 79.86
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 RAYONIX MX-300 2012-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.978590 APS 21-ID-D
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 2.8 30 97.3 0.143 0.143 9.47 115292 112207 -3 36.789
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 97.8 0.539 2.33
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 (All) 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 4GYP 2.8 19.86 1.99 115249 112188 5609 97.61 0.226 0.1762 0.1733 0.1758 0.2313 0.2336 random 27.6265
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 15.787 f_angle_d 1.253 f_chiral_restr 0.074 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26575 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 116
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data collection XDS data reduction PHASER phasing