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Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella bryantii B14, E280A mutant in complex with cellotetraose
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, HANGING DROP 298 1.8 microL of protein solution at 28 mg/mL mixed with 1.8 microL of reservoir solution (0.1 M sodium cacodylate pH 6.3 to 7.1, 0.2 M calcium acetate, 25% PEG8K), then soaking crystals in reservoir solution supplemented with 10 mM cellotetraose for 2 h. Cryoprotectant = paratone-N oil.
Crystal Properties Matthews coefficient Solvent content 1.95 36.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.18 α = 90 b = 85.058 β = 101.4 c = 74.978 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN A200 2014-10-22 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 1.55 19.47 97.1 0.082 14 4 85184
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 1.55 1.63 94.1 0.535 2.9 4
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 1.55 19.456 1.34 85156 4269 97.19 0.1539 0.1525 0.1533 0.1802 0.1789 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 12.278 f_angle_d 1.118 f_chiral_restr 0.046 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5440 Nucleic Acid Atoms Solvent Atoms 987 Heterogen Atoms 93
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing Coot model building