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Akkermansia muciniphila GH95 complexed with fucose (1120; AmGH95B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Structure of AmGH95B (WT)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 22% (w/v) PEG3350
0.1 M C8H19NO5
0.25 M MgCl2
pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.2 61.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.177 α = 90 b = 158.727 β = 90 c = 271.817 γ = 90
Symmetry Space Group P 21 21 21
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 4M 2022-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 1.03 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.77 103.24 99.16 0.2909 0.3142 0.1182 0.993 7.05 7.1 192566 60.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.78 2.81 1 1 0.707 0.565 1.13
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 2.78 103.24 1.34 113576 5632 99.16 0.2119 0.2103 0.2134 0.2437 0.2456 68.66
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 10.8818 f_angle_d 0.5671 f_chiral_restr 0.043 f_plane_restr 0.0051 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23700 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement xia2 data reduction XDS data scaling PHASER phasing