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Crystal structure of GH family 64 laminaripentaose-producing beta-1,3-glucanase from Paenibacillus barengoltzii complexed with laminarihexaose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 Se-derivatized PbBgl64A was prepared and concentrated to 15 mg ml-1 in buffer D contain 5 mM DL-Dithiothreitol (DTT), and optimized crystals were grown in drops containing 2 microliter of protein solution and 0.5 microliter of reservoir solution (14mM sodium cholate, 1.1M di-Ammonium Tartrate pH 7.0) at 293 K
Crystal Properties Matthews coefficient Solvent content 2.76 55.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.561 α = 90 b = 65.191 β = 104.04 c = 61.426 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MAR scanner 345 mm plate 2015-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0093 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.969 28.27 93.45 0.09 0.042 11.21 6.4 33814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.04 64.54 3.41 4.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5H9X 1.969 28.27 1.34 33814 2007 93.45 0.1691 0.1673 0.1682 0.1966 0.1982
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 12.483 f_angle_d 1.126 f_chiral_restr 0.074 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3231 Nucleic Acid Atoms Solvent Atoms 526 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing PHENIX model building