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Complex structure of glycoside hydrolase family 12 beta-1,3-1,4-glucanase with gentiobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.0075M Nike(II) chloride hexahydrate, 0.075M Tris pH 8.5, 0.75M Lithium sulfate monohydrate, 25% glycerol
Crystal Properties Matthews coefficient Solvent content 2.75 55.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.354 α = 90 b = 63.354 β = 90 c = 137.962 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS3 R CdTe 300K 2021-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
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 1.66 57.578 97.7 0.058 47.7 2.3 25816 23.3602478632
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 1.663 1.723 0.058
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 7EE2 1.66079204131 57.5736858431 1.33957029065 25803 1321 75.8577098339 0.211042756125 0.209338463698 0.2095 0.242083423802 0.2424 24.8879428223
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 5.04401832714 f_angle_d 0.817839322555 f_chiral_restr 0.0566332575335 f_bond_d 0.007042556664 f_plane_restr 0.00484110823777
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1774 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 29
Software Software Software Name Purpose HKL-2000 data scaling HKL-2000 data reduction PHENIX model building PHENIX phasing PHENIX refinement