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Crystal structure of Glucoside hydrolase family 64 beta-1,3-glucanase complexed with Laminaritetraose
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 3.52 65.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.486 α = 90 b = 79.486 β = 90 c = 156.662 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 1M 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 2.05 26.1105 97 0.011 31.4 19.2 36584 24.5531518061
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 0.009
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 2.05152566097 26.1103333333 35719 1966 97.512967513 0.21204109066 0.211102238993 0.2088 0.22807826722 0.2273 34.2116635998
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 18.2534124716 f_angle_d 1.22680473454 f_chiral_restr 0.0895214906173 f_bond_d 0.0140469174773 f_plane_restr 0.0078219929382
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2848 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX model building PHENIX phasing