☰ Navigation Tabs
Crystal structure (C2 form) of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 ammonium sulfate 1.4 M
10% dioxane
MMT 0.1 M
Crystal Properties Matthews coefficient Solvent content 3.46 64.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.775 α = 90 b = 46.52 β = 119.5 c = 114.786 γ = 90
Symmetry Space Group C 1 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 PILATUS 2M 2019-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.03316 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.6 28.9 96.7 0.999 12.36 6.5 92515
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 0.75 1.46
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6UB2 1.6 28.9 87867 4625 96.81 0.1817 0.1802 0.1911 0.2098 0.2164 RANDOM 24.877
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] 0.47 -0.29 -2.96 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.791 r_dihedral_angle_4_deg 23.739 r_dihedral_angle_3_deg 10.944 r_dihedral_angle_1_deg 7.276 r_angle_refined_deg 1.693 r_angle_other_deg 1.557 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.791 r_dihedral_angle_4_deg 23.739 r_dihedral_angle_3_deg 10.944 r_dihedral_angle_1_deg 7.276 r_angle_refined_deg 1.693 r_angle_other_deg 1.557 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3724 Nucleic Acid Atoms Solvent Atoms 640 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing