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Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae (AnGH128_VI) in complex with laminaritriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.18 M tri-ammonium citrate, 18% v/v PEG 3350, 0.01 M Cobalt (II) chloride
Crystal Properties Matthews coefficient Solvent content 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.262 α = 90 b = 152.798 β = 90 c = 169.423 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 2.4 49.35 99 0.99 6.24 11.9 123227
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 2.4 2.54 0.602 1.15
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 6UB8 2.4 49.35 117052 6161 99.87 0.2377 0.2367 0.2396 0.2556 0.2578 RANDOM 35.357
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] 6.36 -4.52 -1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.172 r_dihedral_angle_4_deg 19.086 r_dihedral_angle_3_deg 15.005 r_dihedral_angle_1_deg 6.832 r_angle_refined_deg 1.276 r_angle_other_deg 1.11 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.172 r_dihedral_angle_4_deg 19.086 r_dihedral_angle_3_deg 15.005 r_dihedral_angle_1_deg 6.832 r_angle_refined_deg 1.276 r_angle_other_deg 1.11 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20305 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 559
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing