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Crystal structure of Thermoanaerobacterium xylanolyticum GH116 beta-glucosidase with deoxynojirimycin
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 0.14 M Ammonium Sulfate, 21% PEG 3000, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.21 44.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.309 α = 90 b = 54.662 β = 90 c = 83.078 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 2014-04-22 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 1.96 50 99.3 0.078 28.4 6.7 58660
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 1.96 2.03 99.3 0.288 10.2 7.1
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 1.96 50 55692 2926 99.18 0.14842 0.14692 0.1604 0.17679 0.1913 RANDOM 18.599
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] -1.33 1.65 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.702 r_dihedral_angle_4_deg 19.915 r_dihedral_angle_3_deg 12.746 r_dihedral_angle_1_deg 6.236 r_long_range_B_refined 4.944 r_long_range_B_other 4.798 r_scangle_other 2.662 r_mcangle_it 1.9 r_mcangle_other 1.9 r_scbond_it 1.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.702 r_dihedral_angle_4_deg 19.915 r_dihedral_angle_3_deg 12.746 r_dihedral_angle_1_deg 6.236 r_long_range_B_refined 4.944 r_long_range_B_other 4.798 r_scangle_other 2.662 r_mcangle_it 1.9 r_mcangle_other 1.9 r_scbond_it 1.615 r_scbond_other 1.615 r_angle_refined_deg 1.348 r_mcbond_it 1.161 r_mcbond_other 1.16 r_angle_other_deg 0.794 r_chiral_restr 0.083 r_bond_refined_d 0.009 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 6221 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing