☰ Navigation Tabs
Beta-galactosidase from Bacteroides xylanisolvens (complex with alpha-galactose)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8Z43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 potassium thiocyanate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.73 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.831 α = 90 b = 163.831 β = 90 c = 50.857 γ = 90
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 2021-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 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 1.86 41.78 100 0.996 10.3 6.6 57035
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 1.86 1.9 0.711 2.2
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 1.86 41.779 57030 2889 99.928 0.194 0.1925 0.1998 0.2265 0.2322 32.324
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.239 r_dihedral_angle_6_deg 15.271 r_dihedral_angle_3_deg 14.338 r_dihedral_angle_1_deg 6.953 r_lrange_it 6.749 r_lrange_other 6.748 r_scangle_it 5.604 r_scangle_other 5.603 r_scbond_it 3.827 r_scbond_other 3.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.239 r_dihedral_angle_6_deg 15.271 r_dihedral_angle_3_deg 14.338 r_dihedral_angle_1_deg 6.953 r_lrange_it 6.749 r_lrange_other 6.748 r_scangle_it 5.604 r_scangle_other 5.603 r_scbond_it 3.827 r_scbond_other 3.826 r_mcangle_it 3.705 r_mcangle_other 3.705 r_mcbond_it 2.831 r_mcbond_other 2.831 r_angle_refined_deg 1.684 r_angle_other_deg 0.905 r_nbd_refined 0.214 r_symmetry_nbd_other 0.208 r_nbd_other 0.189 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.147 r_xyhbond_nbd_refined 0.137 r_symmetry_nbd_refined 0.1 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.085 r_gen_planes_other 0.012 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_symmetry_xyhbond_nbd_other 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4015 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing