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Crystal structure of beta-glucosidase CaBGL mutant E163Q in complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OGZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 0.1M Bis-Tris, pH 6.5, 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.84 56.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.03 α = 90 b = 221.58 β = 90 c = 236.72 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 CCD ADSC QUANTUM 315r 2019-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97911 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.26 36.92 100 0.071 0.077 0.03 0.998 17.7 6.8 339559
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.32 100 0.607 0.66 0.257 0.881 6.5
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 2.26 36.9 322272 17163 99.94 0.20371 0.20266 0.207 0.2233 0.226 RANDOM 47.911
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] -0.55 -1.66 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.002 r_long_range_B_refined 9.802 r_long_range_B_other 9.802 r_scangle_other 7.658 r_mcangle_it 5.839 r_mcangle_other 5.839 r_dihedral_angle_1_deg 5.714 r_scbond_it 5.132 r_scbond_other 5.128 r_mcbond_it 4.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.002 r_long_range_B_refined 9.802 r_long_range_B_other 9.802 r_scangle_other 7.658 r_mcangle_it 5.839 r_mcangle_other 5.839 r_dihedral_angle_1_deg 5.714 r_scbond_it 5.132 r_scbond_other 5.128 r_mcbond_it 4.292 r_mcbond_other 4.291 r_dihedral_angle_2_deg 4.226 r_angle_refined_deg 1.455 r_angle_other_deg 0.505 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 45436 Nucleic Acid Atoms Solvent Atoms 960 Heterogen Atoms 330
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction PDB_EXTRACT data extraction PHASER phasing