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Crystal structure of Thermoanaerobacterium xylanolyticum GH116 beta-glucosidase with glucose
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, HANGING DROP 5.5 288 0.16 M Ammonium Sulfate, 24% PEG 4000, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.22 44.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.825 α = 90 b = 54.566 β = 90 c = 83.213 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 CCD RAYONIX MX-300 2014-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 50 95.1 0.078 37.7 6.4 66687
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 89.1 0.453 8.3 6.2
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 1.85 50 63333 3292 95.02 0.14867 0.14715 0.1599 0.17799 0.1887 RANDOM 21.124
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.131 r_dihedral_angle_4_deg 18.68 r_dihedral_angle_3_deg 12.751 r_dihedral_angle_1_deg 6.342 r_long_range_B_refined 4.716 r_long_range_B_other 4.583 r_scangle_other 2.935 r_mcangle_it 2.006 r_mcangle_other 2.006 r_scbond_it 1.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.131 r_dihedral_angle_4_deg 18.68 r_dihedral_angle_3_deg 12.751 r_dihedral_angle_1_deg 6.342 r_long_range_B_refined 4.716 r_long_range_B_other 4.583 r_scangle_other 2.935 r_mcangle_it 2.006 r_mcangle_other 2.006 r_scbond_it 1.819 r_scbond_other 1.819 r_angle_refined_deg 1.377 r_mcbond_it 1.268 r_mcbond_other 1.267 r_angle_other_deg 0.792 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 6215 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing