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Crystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with unreacted beta Cyclophellitol Cyclosulfate probe ME711
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 100 mM MES pH 6.5
0.2 M Ammonium Sulfate
16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.17 α = 90 b = 53.731 β = 90 c = 83.138 γ = 90
Symmetry Space Group P 21 21 2
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 6M-F 2017-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.16 59.39 100 0.072 0.04 0.999 11.3 7.9 275502
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.16 1.18 100 2.09 1.14 0.515 1 7.5
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 5fjs 1.16 59.39 261588 13813 99.96 0.14009 0.13887 0.1374 0.16298 0.1615 Same as 5NPF 17.91
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] -0.36 -1.65 2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.982 r_sphericity_free 30.854 r_dihedral_angle_4_deg 19.592 r_sphericity_bonded 17.621 r_dihedral_angle_3_deg 12.05 r_long_range_B_refined 6.575 r_long_range_B_other 6.575 r_dihedral_angle_1_deg 6.543 r_rigid_bond_restr 2.853 r_scangle_other 2.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.982 r_sphericity_free 30.854 r_dihedral_angle_4_deg 19.592 r_sphericity_bonded 17.621 r_dihedral_angle_3_deg 12.05 r_long_range_B_refined 6.575 r_long_range_B_other 6.575 r_dihedral_angle_1_deg 6.543 r_rigid_bond_restr 2.853 r_scangle_other 2.703 r_scbond_it 2.301 r_scbond_other 2.301 r_mcangle_other 2.248 r_mcangle_it 2.246 r_angle_refined_deg 1.785 r_mcbond_it 1.778 r_mcbond_other 1.758 r_angle_other_deg 1.031 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6225 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling Coot model building MOLREP phasing