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ZgGH129 from Zobellia galactanivorans in complex with the inhibitor AD-DGJ (3,6-anhydro-D-1-deoxygalactonojirimycin).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2:1 ratio
0.14M Na/K-tartrate, 14% PEG 3350
1.63 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.83 56.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.204 α = 90 b = 106.492 β = 113.797 c = 165.341 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 EIGER X 9M 2018-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9786 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 48.42 99.3 0.064 0.998 10.9 2.9 303236 23.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.93 99.3 0.433 0.848 3 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.83 41.32 1.34 303054 15098 99.17 0.1374 0.1361 0.1369 0.1624 0.1633 27.81
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 f_dihedral_angle_d 13.097 f_angle_d 1.1696 f_chiral_restr 0.0787 f_bond_d 0.0134 f_plane_restr 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20922 Nucleic Acid Atoms Solvent Atoms 2921 Heterogen Atoms 201
Software Software Software Name Purpose XDS data reduction Aimless data scaling Coot model building MOLREP phasing PHENIX refinement