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Beta-galactosidase from Bacteroides xylanisolvens (complex with methyl beta-galactopyranose)
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 2.68 54.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 231.765 α = 90 b = 50.839 β = 96.099 c = 229.445 γ = 90
Symmetry Space Group C 1 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 PILATUS3 6M 2021-05-29 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 1.94 45.91 98.2 0.997 8.1 3.1 194503
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 1.94 1.97 0.768 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 1.94 45.629 194501 9831 98.081 0.213 0.2113 0.2195 0.251 0.2561 24.79
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] 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.931 r_dihedral_angle_3_deg 14.844 r_dihedral_angle_2_deg 8.41 r_dihedral_angle_1_deg 7.218 r_lrange_it 5.562 r_lrange_other 5.523 r_scangle_it 4.331 r_scangle_other 4.331 r_mcangle_it 2.954 r_mcangle_other 2.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.931 r_dihedral_angle_3_deg 14.844 r_dihedral_angle_2_deg 8.41 r_dihedral_angle_1_deg 7.218 r_lrange_it 5.562 r_lrange_other 5.523 r_scangle_it 4.331 r_scangle_other 4.331 r_mcangle_it 2.954 r_mcangle_other 2.954 r_scbond_it 2.77 r_scbond_other 2.77 r_mcbond_it 2.05 r_mcbond_other 2.05 r_angle_refined_deg 1.535 r_angle_other_deg 0.841 r_nbd_other 0.252 r_nbd_refined 0.206 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.173 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.119 r_symmetry_xyhbond_nbd_other 0.113 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.076 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16098 Nucleic Acid Atoms Solvent Atoms 1329 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing