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Crystal structure (P21 form) of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritriose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 lithium sulfate 1.4 M
2% PEG400
Tris 0.1 M
Crystal Properties Matthews coefficient Solvent content 1.86 34.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.806 α = 90 b = 47.71 β = 110.81 c = 52.517 γ = 90
Symmetry Space Group P 1 21 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 1.033120 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 1.3 49.09 99.8 0.995 7.42 5.85 52180
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 1.3 1.38 0.569
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.3 49.09 49571 2609 99.89 0.1692 0.1686 0.1684 0.1815 0.181 RANDOM 8.978
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] 0.18 -0.04 -0.43 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.184 r_dihedral_angle_4_deg 18.47 r_dihedral_angle_3_deg 10.894 r_dihedral_angle_1_deg 7.219 r_angle_other_deg 2.359 r_angle_refined_deg 1.25 r_mcangle_it 0.955 r_mcbond_it 0.582 r_mcbond_other 0.578 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.184 r_dihedral_angle_4_deg 18.47 r_dihedral_angle_3_deg 10.894 r_dihedral_angle_1_deg 7.219 r_angle_other_deg 2.359 r_angle_refined_deg 1.25 r_mcangle_it 0.955 r_mcbond_it 0.582 r_mcbond_other 0.578 r_chiral_restr 0.06 r_bond_other_d 0.036 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_refined_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1891 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing