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Crystal structure of the UcaD lectin-binding domain in complex with fucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other UcaD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M sodium citrate buffer pH 4.5-5.5, 2-3 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.52 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.472 α = 90 b = 79.472 β = 90 c = 70.227 γ = 90
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 2018-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.5 39.74 99.8 0.064 0.066 0.018 0.999 18.3 13.8 34590 17.65
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 1.5 1.53 0.667 0.694 0.187 0.895 2.5
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 UcaD 1.5 39.74 1.38 34587 1999 99.77 0.1634 0.1626 0.162 0.1761 0.1758 21.22
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 11.4473 f_angle_d 0.9361 f_chiral_restr 0.0622 f_plane_restr 0.0089 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1450 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing