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Structure of beta-glycosidase from Sulfolobus solfataricus in complex with C5a-fluoro-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 293 10 - 13 % PEG 4000, 0.1 M Sodium Acetate, 0.2M Ammonium Acetate, 5% ethylene glycol.
Crystal Properties Matthews coefficient Solvent content 3.44 64.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.265 α = 90 b = 168.265 β = 90 c = 95.504 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 1.83 47.8 99.9 0.027 1 11.6 10.2 136568
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 1.83 1.88 99.9 1.115 0.28 0.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1uwr 1.83 45.419 136532 6942 99.912 0.209 0.2074 0.2077 0.2423 0.2421 41.337
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] -0.871 -0.436 -0.871 2.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.159 r_dihedral_angle_4_deg 18.695 r_dihedral_angle_3_deg 16.339 r_dihedral_angle_1_deg 7.288 r_lrange_it 6.453 r_lrange_other 6.437 r_scangle_it 5.416 r_scangle_other 5.415 r_mcangle_it 4.61 r_mcangle_other 4.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.159 r_dihedral_angle_4_deg 18.695 r_dihedral_angle_3_deg 16.339 r_dihedral_angle_1_deg 7.288 r_lrange_it 6.453 r_lrange_other 6.437 r_scangle_it 5.416 r_scangle_other 5.415 r_mcangle_it 4.61 r_mcangle_other 4.61 r_scbond_it 4.01 r_scbond_other 4.01 r_mcbond_it 3.685 r_mcbond_other 3.675 r_angle_refined_deg 1.668 r_angle_other_deg 1.392 r_nbd_refined 0.208 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.18 r_nbd_other 0.152 r_xyhbond_nbd_refined 0.147 r_symmetry_xyhbond_nbd_refined 0.128 r_symmetry_nbd_refined 0.122 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7926 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing