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Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella bryantii B14, in complex with an inhibitory N-bromoacetylglycosylamine derivative of XXXG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 28 mg/mL plus 6.6 mM EDTA, incubated 4 degrees overnight, then added 8M XXXG-NHCOCH2Br (inhibitor), incubated at 37 degrees for 3 h, then 0.5 microL of this solution was mixed with 0.5 microL of reservoir solution: 0.2 M calcium chloride, 20% (w/v) PEG3350. Cryoprotectant = paratone-N oil.
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.192 α = 76.39 b = 49.015 β = 89.98 c = 85.972 γ = 66.8
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 RIGAKU SATURN A200 2014-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.8 31.921 92.8 0.06 11.47 1.9 60113
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 1.8 1.85 86.5 0.309 2.13 1.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3VDH 1.8 31.921 1.96 60096 1850 92.7 0.1646 0.1633 0.1672 0.2041 0.2064 Random selection
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 12.508 f_angle_d 1.189 f_chiral_restr 0.046 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5444 Nucleic Acid Atoms Solvent Atoms 750 Heterogen Atoms 302
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing Coot model building