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Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) in complex with laminaritetraose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 1.6 M ammonium sulfate
5% dioxane
0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.87 34.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.871 α = 90 b = 47.678 β = 110.42 c = 52.549 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 2019-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.03318 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.25 50 99.1 0.109 0.999 10.54 5.9 58956
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.33 98.2 1.302 0.659 5.6
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.25 49.25 58538 2927 99.6 0.174 0.183 0.191 0.1986 13.5
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] 0.199 0.448 -0.811 0.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.707 r_dihedral_angle_4_deg 18.406 r_dihedral_angle_3_deg 11.474 r_dihedral_angle_1_deg 7.282 r_angle_other_deg 3.072 r_scangle_it 1.585 r_scangle_other 1.584 r_angle_refined_deg 1.272 r_mcangle_it 1.13 r_mcangle_other 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.707 r_dihedral_angle_4_deg 18.406 r_dihedral_angle_3_deg 11.474 r_dihedral_angle_1_deg 7.282 r_angle_other_deg 3.072 r_scangle_it 1.585 r_scangle_other 1.584 r_angle_refined_deg 1.272 r_mcangle_it 1.13 r_mcangle_other 1.13 r_scbond_it 1.095 r_scbond_other 1.094 r_mcbond_it 0.768 r_mcbond_other 0.768 r_nbd_refined 0.193 r_nbd_other 0.189 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.062 r_bond_other_d 0.036 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1897 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing