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Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae (AnGH128_VI) with laminaribiose at the surface-binding site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.18 M tri-ammonium citrate, 18% v/v PEG 3,350, 0.01 M Cobalt (II) chloride
Crystal Properties Matthews coefficient Solvent content 2.54 51.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.349 α = 90 b = 152.733 β = 90 c = 169.135 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2019-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458570 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 2.35 50 99.9 0.98 4.8 6.7 130821
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 2.35 2.49 0.433
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 2.35 49.3 130808 6541 99.8 0.265 0.2663 0.301 0.3004 33.87
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] 3.831 -2.842 -0.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.255 r_dihedral_angle_4_deg 18.212 r_dihedral_angle_3_deg 15.859 r_dihedral_angle_1_deg 6.534 r_angle_other_deg 2.474 r_angle_refined_deg 1.193 r_mcangle_it 0.882 r_mcangle_other 0.882 r_scangle_it 0.556 r_scangle_other 0.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.255 r_dihedral_angle_4_deg 18.212 r_dihedral_angle_3_deg 15.859 r_dihedral_angle_1_deg 6.534 r_angle_other_deg 2.474 r_angle_refined_deg 1.193 r_mcangle_it 0.882 r_mcangle_other 0.882 r_scangle_it 0.556 r_scangle_other 0.556 r_mcbond_it 0.47 r_mcbond_other 0.47 r_scbond_it 0.291 r_scbond_other 0.291 r_nbd_refined 0.165 r_nbd_other 0.162 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.098 r_chiral_restr 0.042 r_bond_other_d 0.035 r_gen_planes_other 0.003 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 20310 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing