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ZgGH129 from Zobellia galactanivorans in complex with the inhibitor ADG-IF (3,6-anhydro-D-galacto-isofagomine).
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 1.63 mg/ml
2:1 ratio
0.14M Na/K-tartrate, 14% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.8 56.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 218.781 α = 90 b = 106.12 β = 113.924 c = 164.695 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 16M 2020-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9801 SOLEIL PROXIMA 1
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 1.99 48.22 98.3 0.155 0.995 8.3 7 232909 33.35
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 1.99 2.09 95.3 1.168 0.689 1.6 7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.99 47.38 1.34 232786 11665 98.17 0.1555 0.1539 0.1851 0.1874 34.74
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 12.4307 f_angle_d 1.1835 f_chiral_restr 0.0881 f_bond_d 0.0112 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20787 Nucleic Acid Atoms Solvent Atoms 2266 Heterogen Atoms 285
Software Software Software Name Purpose XDS data reduction Aimless data scaling Coot model building MOLREP phasing PHENIX refinement