☰ Navigation Tabs
Crystal structure of the FimH-binding decoy module of human glycoprotein 2 (GP2) (crystal form III)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P6S Refined model of crystal form II of the same protein (PDB D_1292117105)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 5% (w/v) PEG 20K, 25% (w/v) 1,1,1-tris(hydroxymethyl) propane, 0.1 M MOPSO/bis-tris pH 6.5, 1% (w/v) NDSB 195, 0.01 M spermine, 0.01 M spermidine, 0.01 M 1,4-diaminobutane, 0.01 M DL-ornithine, 20 mM Na-HEPES pH 7.5, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.35 47.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.15 α = 90 b = 33.66 β = 111.839 c = 59.63 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 4M 2021-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.96770 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 1.4 28.97 98.4 0.104 0.112 0.042 1 8.6 6.9 32721 18.91
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 1.4 1.474 96.84 3.379 3.663 1.396 0.485 0.6 6.7
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 Refined model of crystal form II of the same protein (PDB D_1292117105) 1.4 28.97 1.34 32510 2017 98.38 0.1966 0.1947 0.1895 0.2236 0.2184 31.34
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 12.2532 f_angle_d 0.6748 f_chiral_restr 0.0685 f_plane_restr 0.0086 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1060 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 87
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing Coot model building ISOLDE refinement PHENIX refinement