☰ Navigation Tabs
Crystal structure of the FimH-binding decoy module of human glycoprotein 2 (GP2) (crystal form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold2 model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25% (v/v) ethylene glycol, 20 mM Na-HEPES pH 7.5, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.17 43.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.04 α = 68.75 b = 46.53 β = 75.873 c = 57.44 γ = 72.398
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 PILATUS 6M 2020-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.00523 ESRF ID23-1
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 1.9 52.92 96.6 0.099 0.118 0.063 0.99 8.8 3.5 22914 20.06
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 1.9 1.97 91.4 0.509 0.611 0.333 0.89 2.6 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 AlphaFold2 model 1.9 52.92 1.98 22860 1579 96.56 0.2369 0.2337 0.2485 0.2805 0.2861 28.66
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 11.7342 f_angle_d 0.7253 f_chiral_restr 0.0507 f_plane_restr 0.0079 f_bond_d 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2056 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 106
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing Coot model building ISOLDE refinement PHENIX refinement