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Crystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with beta Cyclophellitol Cyclosulfate probe ME594
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2 M Ammonium Sulfate, 23% PEG 3000, 0.1 M MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.18 α = 90 b = 53.81 β = 90 c = 83.3 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 2016-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.38 53.81 99.3 0.069 0.03 0.999 15.1 6.1 163829
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 1.38 1.42 93.5 0.968 0.59 0.508 1.3 3.1
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 5bvu 1.38 51.57 155502 8245 99.22 0.12724 0.12545 0.1265 0.1605 0.1602 RANDOM 19.218
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] 1.59 -1.53 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.548 r_sphericity_free 33.105 r_dihedral_angle_4_deg 22.629 r_sphericity_bonded 16.98 r_dihedral_angle_3_deg 12.168 r_dihedral_angle_1_deg 6.588 r_long_range_B_other 3.942 r_long_range_B_refined 3.94 r_scangle_other 3.393 r_scbond_it 2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.548 r_sphericity_free 33.105 r_dihedral_angle_4_deg 22.629 r_sphericity_bonded 16.98 r_dihedral_angle_3_deg 12.168 r_dihedral_angle_1_deg 6.588 r_long_range_B_other 3.942 r_long_range_B_refined 3.94 r_scangle_other 3.393 r_scbond_it 2.91 r_scbond_other 2.901 r_mcangle_other 2.885 r_mcangle_it 2.884 r_rigid_bond_restr 2.468 r_mcbond_it 2.358 r_mcbond_other 2.352 r_angle_refined_deg 1.74 r_angle_other_deg 1.022 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 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 6185 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing