☰ Navigation Tabs
GH29 from Akkermansia muciniphila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 CHES-NaOH (0.1 M), pH 9.5 and sodium citrate (1M).
Crystal Properties Matthews coefficient Solvent content 2.04 39.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.109 α = 90 b = 69.4 β = 90 c = 143.431 γ = 90
Symmetry Space Group P 2 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 16M 2023-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9201 NSLS-II 17-ID-1
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 2.6 60.11 99.8 0.262 0.297 0.136 0.931 6.8 5.1 19121 34.81
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 2.6 2.67 100 1.052 1.189 0.537 0.528 2.5
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 2.6 60.11 1.34 18904 1890 98.79 0.192 0.1846 0.1884 0.2577 0.2571 34.96
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 16.7365 f_angle_d 0.88 f_chiral_restr 0.0502 f_plane_restr 0.0078 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3743 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing autoPROC data processing