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Complex structure of glycoside hydrolase family 12 beta-1,3-1,4-glucanase with cellobiose
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 2.87 57.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.376 α = 90 b = 64.376 β = 90 c = 139.361 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 1.477 28.79 96.1 0.048 33.1 4.9 39513 18.3210852869
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 1.479 1.531 0.048
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 1.47798052862 28.7898224239 1.38767695787 39496 2039 79.1281003326 0.18414087079 0.182362234208 0.1825 0.216795213779 0.2155 23.7098459548
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 7.50206795568 f_angle_d 0.892161062428 f_chiral_restr 0.0998518532288 f_bond_d 0.00723232642037 f_plane_restr 0.00471718446176
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1774 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX model building PHENIX phasing