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Crystal structure of a GH128 (subgroup III) curdlan-specific exo-beta-1,3-glucanase from Blastomyces gilchristii (BgGH128_III) in complex with laminaribiose at -2 and -1 subsites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.05 M Potassium di-hydrogen phosphate 24% Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 1.85 33.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.561 α = 90 b = 34.231 β = 104.88 c = 56.351 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 2017-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45855 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 1.75 32.11 98.9 0.999 24.65 4.61 18575
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 1.75 1.86 96.2 0.976 4.2 4.14
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 6UAY 1.75 32.11 17645 929 99 0.2226 0.2203 0.2276 0.2647 0.2712 RANDOM 33.877
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] 2.09 0.72 -0.4 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.338 r_dihedral_angle_4_deg 22.779 r_dihedral_angle_3_deg 16.217 r_dihedral_angle_1_deg 7.525 r_angle_refined_deg 1.958 r_angle_other_deg 1.447 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.338 r_dihedral_angle_4_deg 22.779 r_dihedral_angle_3_deg 16.217 r_dihedral_angle_1_deg 7.525 r_angle_refined_deg 1.958 r_angle_other_deg 1.447 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1747 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing