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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 -3 and -2 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, HANGING DROP 291 0.05 M Potassium di-hydrogen phosphate, 24% Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 1.76 30.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.323 α = 69.67 b = 60.804 β = 78.24 c = 63.545 γ = 77.86
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 2017-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458540 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 1.6 35.49 86.2 0.994 13.35 3.3 87019
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 1.6 1.7 86.8 0.986 7.48 3.2
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 1.6 35.49 82649 4350 86.27 0.1623 0.1604 0.1722 0.1969 0.2072 RANDOM 16.249
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] -1.11 -0.25 -0.27 0.68 -0.32 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.126 r_dihedral_angle_4_deg 18.668 r_dihedral_angle_1_deg 18.229 r_dihedral_angle_3_deg 12.832 r_angle_refined_deg 1.945 r_angle_other_deg 1.599 r_chiral_restr 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.126 r_dihedral_angle_4_deg 18.668 r_dihedral_angle_1_deg 18.229 r_dihedral_angle_3_deg 12.832 r_angle_refined_deg 1.945 r_angle_other_deg 1.599 r_chiral_restr 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6988 Nucleic Acid Atoms Solvent Atoms 1096 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing