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Structure of beta-glycosidase from Sulfolobus solfataricus in complex with C5a-bromo-valienide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 10 - 13 % PEG 4000, 0.1 M Sodium Acetate, 0.2M Ammonium Acetate, 5% ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 3.43 64.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.088 α = 90 b = 168.088 β = 90 c = 95.548 γ = 120
Symmetry Space Group P 31 2 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 EIGER X 16M 2021-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.58 46.4 99.9 0.025 1 12.2 10.1 211061
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.62 100 0.805 0.37 0.7
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1UWR 1.58 43.301 211023 10231 99.868 0.19 0.1894 0.2123 0.2414 33.763
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] -0.345 -0.173 -0.345 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.173 r_dihedral_angle_4_deg 16.775 r_dihedral_angle_3_deg 14.512 r_dihedral_angle_1_deg 6.956 r_lrange_it 6.55 r_lrange_other 6.548 r_scangle_it 5.712 r_scangle_other 5.711 r_scbond_it 4.072 r_scbond_other 4.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.173 r_dihedral_angle_4_deg 16.775 r_dihedral_angle_3_deg 14.512 r_dihedral_angle_1_deg 6.956 r_lrange_it 6.55 r_lrange_other 6.548 r_scangle_it 5.712 r_scangle_other 5.711 r_scbond_it 4.072 r_scbond_other 4.072 r_mcangle_other 3.701 r_mcangle_it 3.699 r_mcbond_it 3.031 r_mcbond_other 3.028 r_angle_refined_deg 1.906 r_angle_other_deg 1.502 r_nbd_other 0.229 r_nbd_refined 0.209 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.175 r_xyhbond_nbd_refined 0.12 r_symmetry_xyhbond_nbd_refined 0.099 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7941 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing