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Crystal structure of E56A mutant of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides thetaiotaomicron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E8M PDB entry 3e8m
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 100 mM Bis-Tris, 200 mM magnesium chloride, 23% polyethylene glycol 3350. The crystal was dragged through paratone prior to flash-cooling, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.31 46.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.941 α = 90 b = 94.116 β = 90 c = 161.497 γ = 90
Symmetry Space Group P 2 2 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 Bruker Platinum 135 Helios multi-layer optics 2009-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
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 2.28 37.1 99.9 0.0878 11.6 6.21 62511 62511 2 2
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 2.28 2.37 100 0.4648 2.2 4.63 3877
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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 entry 3e8m 2.28 37.1 62511 3557 93.24 0.1971 0.1954 0.1894 0.2493 0.2454 random 25.75
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] -3.193 -0.2331 3.4261
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.39 f_angle_d 1.015 f_chiral_restr 0.07 f_bond_d 0.007 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10320 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 8
Software Software Software Name Purpose PROTEUM PLUS data collection MOLREP phasing PHENIX refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling