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Beta-galactosidase from Bacteroides xylanisolvens (E350G, ligand-free)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 sodium citrate tribasic dihydrate, PEG 3350, bis-Tris propane
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.699 α = 90 b = 51.062 β = 90.415 c = 180.085 γ = 90
Symmetry Space Group I 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 2019-12-10 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 1.91 48.198 99.9 0.999 15.8 6.6 102654
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 1.91 1.94 0.754 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 1.91 48.152 102647 5220 99.843 0.176 0.1742 0.1834 0.202 0.2077 27.594
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] 0.02 -0.023 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.125 r_dihedral_angle_3_deg 13.8 r_dihedral_angle_2_deg 7.304 r_dihedral_angle_1_deg 7.15 r_lrange_it 6.153 r_lrange_other 6.153 r_scangle_it 5.097 r_scangle_other 5.097 r_scbond_it 3.403 r_scbond_other 3.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.125 r_dihedral_angle_3_deg 13.8 r_dihedral_angle_2_deg 7.304 r_dihedral_angle_1_deg 7.15 r_lrange_it 6.153 r_lrange_other 6.153 r_scangle_it 5.097 r_scangle_other 5.097 r_scbond_it 3.403 r_scbond_other 3.403 r_mcangle_it 3.154 r_mcangle_other 3.154 r_mcbond_it 2.348 r_mcbond_other 2.347 r_angle_refined_deg 1.682 r_angle_other_deg 0.588 r_symmetry_nbd_refined 0.249 r_nbd_refined 0.216 r_nbd_other 0.2 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.155 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.027 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8428 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing