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Glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus (ligand-free)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Bis-Tris (pH 5.5), 0.2 M ammonium acetate, 15% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.858 α = 90 b = 97.756 β = 90 c = 184.874 γ = 90
Symmetry Space Group P 21 21 21
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 S 2M 2020-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 48.43 100 0.991 8.8 6.6 89749
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 100 0.685
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 46.261 89668 4438 99.936 0.233 0.232 0.2568 0.221 25.474
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] -0.448 -2.656 3.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.719 r_dihedral_angle_6_deg 13.108 r_dihedral_angle_1_deg 6.464 r_dihedral_angle_2_deg 4.976 r_lrange_it 1.562 r_lrange_other 1.562 r_angle_refined_deg 0.863 r_mcangle_it 0.772 r_mcangle_other 0.772 r_angle_other_deg 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.719 r_dihedral_angle_6_deg 13.108 r_dihedral_angle_1_deg 6.464 r_dihedral_angle_2_deg 4.976 r_lrange_it 1.562 r_lrange_other 1.562 r_angle_refined_deg 0.863 r_mcangle_it 0.772 r_mcangle_other 0.772 r_angle_other_deg 0.54 r_scangle_it 0.483 r_scangle_other 0.483 r_mcbond_it 0.41 r_mcbond_other 0.41 r_scbond_it 0.24 r_scbond_other 0.24 r_symmetry_nbd_other 0.209 r_nbd_refined 0.185 r_nbtor_refined 0.176 r_nbd_other 0.175 r_xyhbond_nbd_refined 0.109 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_nbd_refined 0.102 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.047 r_symmetry_xyhbond_nbd_other 0.033 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12240 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement XDS data reduction MOLREP phasing ARP/wARP model building Aimless data scaling