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GH5-4 broad specificity endoglucanase from Bacteroides salanitronis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YHE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 200 nL of a solution containing 59 mg/mL protein, 50 nM NaCl, 5 mM MOPS buffer pH 7 was mixed with 130 nL reservoir solution containing 16% PEG3350, 0.2 M MgCl2, and 0.1 M sodium acetate buffer at pH 5. Vapor diffusion in MRC plates. Crystals appeared within a few days, and were cryo-protected using a reservoir solution supplemented to 35% PEG3350.
Crystal Properties Matthews coefficient Solvent content 2.08 40.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.48 α = 90 b = 92.31 β = 90 c = 95.15 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 2016-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.7749 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 1.05 29.24 99.19 0.05084 0.053 0.01479 1 22.62 12.1 165260 11.23
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 1.05 1.088 93 0.832 0.9114 0.3576 0.621 1.68 6.1
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 4yhe 1.05 29.24 1.34 165248 3534 99.19 0.1389 0.1387 0.1396 0.1453 0.1429 15.57
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 13.067 f_angle_d 0.882 f_chiral_restr 0.075 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2966 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing