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GH5-4 broad specificity endoglucanase from an uncultured bacterium
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 293 Protein 37 mg/mL in 10 mM MOPS buffer at pH 7, 50 mM NaCl was mixed with an equal volume of reservoir solution with 0.15M DL Malic acid, 20% PEG 3350. Sample was cryoprotected with reservoir supplemented to 35% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.56 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.64 α = 90 b = 91.89 β = 90 c = 170.85 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2017-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.774901 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.5 36.52 99.96 0.07386 0.07679 0.02085 1 19.45 13.6 140750 21.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.554 99.94 1.39 1.444 0.3862 0.746 1.66 13.9
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 3vdh 1.5 36.52 1.35 140711 1980 99.97 0.148 0.1477 0.1497 0.1699 0.1715 28.92
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 13.1147 f_angle_d 0.967 f_chiral_restr 0.079 f_bond_d 0.0072 f_plane_restr 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5890 Nucleic Acid Atoms Solvent Atoms 1048 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASES phasing