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Crystal structure of Glycoside Hydrolases family 64 beta-1,3-glucanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GD0
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 3.5 64.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.989 α = 90 b = 78.989 β = 90 c = 157.647 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 16M 2021-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 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 1.9 24.57 99 0.079 43.8 19.4 45108 18.2844256299
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 1.9 1.975
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 3GD0 1.90697329759 24.5673366606 44871 1990 99.3204657134 0.201425243383 0.199628394356 0.1994 0.240459142987 0.2399 21.7504805606
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 3.26517064087 f_angle_d 0.947027950554 f_chiral_restr 0.0500921474916 f_bond_d 0.00798211652398 f_plane_restr 0.00644336049534
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2846 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data collection PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX model building PHENIX phasing