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The Michaelis complex of ZgGH129 D486N from Zobellia galactanivorans with neo-b/k-oligo-carrageenan tetrasaccharide (beta-kappa neo-oligo-carrageenan DP4).
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 2.75 55.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.734 α = 90 b = 105.943 β = 111.233 c = 213.664 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 EIGER X 16M 2019-04-25 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 2.29 47.89 100 0.161 0.996 9.2 6.9 152074 42.15
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 2.29 2.33 100 1.5 0.551 1.5 7.1
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 2.29 47.82 1.34 152064 7610 99.97 0.1705 0.1688 0.171 0.2016 0.2046 44.91
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 16.0044 f_angle_d 0.8103 f_chiral_restr 0.0512 f_bond_d 0.0052 f_plane_restr 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20951 Nucleic Acid Atoms Solvent Atoms 1146 Heterogen Atoms 250
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling Coot model building MOLREP phasing