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High-resolution crystal structure of exo-beta-(1,3)-glucanase from Aspergillus oryzae (AoBgl) as a complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 291 0.2M Sodium tartrate dibasic dihydrate, 20% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.29 α = 90 b = 81.29 β = 90 c = 114.74 γ = 120
Symmetry Space Group P 32 2 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 CCD MAR CCD 300 mm 2024-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97893 RRCAT INDUS-2 PX-BL21
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 1.2 20 98.3 0.999 13.72 10.17 134619
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 1.2 1.4 0.858
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-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 1.2 19.53 127482 6709 97.95 0.1622 0.16101 0.1631 0.18505 0.1891 RANDOM 9.875
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] -0.62 -0.31 -0.62 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.08 r_dihedral_angle_1_deg 6.594 r_dihedral_angle_2_deg 6.135 r_rigid_bond_restr 4.527 r_long_range_B_refined 3.935 r_long_range_B_other 2.578 r_angle_refined_deg 1.791 r_scangle_other 1.491 r_scbond_it 1.103 r_scbond_other 1.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.08 r_dihedral_angle_1_deg 6.594 r_dihedral_angle_2_deg 6.135 r_rigid_bond_restr 4.527 r_long_range_B_refined 3.935 r_long_range_B_other 2.578 r_angle_refined_deg 1.791 r_scangle_other 1.491 r_scbond_it 1.103 r_scbond_other 1.102 r_mcangle_it 0.969 r_mcangle_other 0.968 r_mcbond_it 0.716 r_mcbond_other 0.712 r_angle_other_deg 0.636 r_chiral_restr 0.111 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2951 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing