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Crystal structure of GH family 64 beta-1,3-glucanase complexed with Laminaritriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.1M sodium malonate pH 7.0, 0.1M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.83 67.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.68 α = 90 b = 81.68 β = 90 c = 161.24 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS EIGER2 X 9M 2021-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.07 25.38 97 0.08 21.6 18.6 38667 50.9503395566
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 2.07 2.1221 0.079
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 7VTK 2.07037904157 25.3769832441 37638 1953 97.2407378701 0.208790400183 0.207707837251 0.2062 0.228699693042 0.2277 63.8672822637
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 16.8956616717 f_angle_d 1.04008680671 f_chiral_restr 0.0633109708745 f_bond_d 0.00819108461435 f_plane_restr 0.00714041285465
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2838 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing