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Glycoside hydrolase family 1 beta-glucosidase (E318G mutant) from Streptomyces griseus (sophorose complex)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8KAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Bis-Tris propane (pH 6.5), 0.3 M sodium formate, 18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.793 α = 90 b = 100.179 β = 102.868 c = 96.048 γ = 90
Symmetry Space Group P 1 21 1
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 2022-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.13 46.824 98.7 0.995 10.4 3.4 93387
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 2.13 2.17 0.637
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.13 46.818 93364 4704 98.515 0.183 0.1808 0.1899 0.2278 0.2327 28.303
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] -0.007 0.002 0.002 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.723 r_dihedral_angle_3_deg 14.492 r_dihedral_angle_2_deg 9.658 r_dihedral_angle_1_deg 6.883 r_lrange_it 5.929 r_lrange_other 5.897 r_scangle_it 4.751 r_scangle_other 4.751 r_mcangle_it 3.702 r_mcangle_other 3.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.723 r_dihedral_angle_3_deg 14.492 r_dihedral_angle_2_deg 9.658 r_dihedral_angle_1_deg 6.883 r_lrange_it 5.929 r_lrange_other 5.897 r_scangle_it 4.751 r_scangle_other 4.751 r_mcangle_it 3.702 r_mcangle_other 3.702 r_scbond_it 3.182 r_scbond_other 3.181 r_mcbond_it 2.622 r_mcbond_other 2.621 r_angle_refined_deg 1.666 r_angle_other_deg 0.926 r_nbd_refined 0.238 r_nbd_other 0.215 r_symmetry_nbd_other 0.214 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.133 r_symmetry_xyhbond_nbd_refined 0.111 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.036 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_chiral_restr_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12145 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing ARP/wARP model building