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Beta-glucosidase from Thermoanaerobacterium xylolyticum GH116 in complex with Gluco-1H-imidazole
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 291 PEG 3350, ammonium sulphate, Bis-tris
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.617 α = 90 b = 54.09 β = 90 c = 83.559 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 PILATUS3 6M 2017-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 2.3 88.76 99.9 0.318 0.126 0.949 5.5 7.6 36706
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 2.3 2.38 99.7 1.63 0.64 0.748 2 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 5BVU 2.1 88.97 44762 2286 98.07 0.20224 0.19978 0.2093 0.25094 0.2595 RANDOM 25.56
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] -3.29 2.78 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.658 r_dihedral_angle_4_deg 18.103 r_dihedral_angle_3_deg 14.442 r_dihedral_angle_1_deg 7.12 r_long_range_B_refined 4.304 r_long_range_B_other 4.303 r_scangle_other 2.894 r_mcangle_it 2.786 r_mcangle_other 2.785 r_scbond_it 1.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.658 r_dihedral_angle_4_deg 18.103 r_dihedral_angle_3_deg 14.442 r_dihedral_angle_1_deg 7.12 r_long_range_B_refined 4.304 r_long_range_B_other 4.303 r_scangle_other 2.894 r_mcangle_it 2.786 r_mcangle_other 2.785 r_scbond_it 1.956 r_scbond_other 1.956 r_mcbond_it 1.91 r_mcbond_other 1.91 r_angle_refined_deg 1.711 r_angle_other_deg 1.038 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 6100 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing