6MAP

F9 Pilus Adhesin FmlH Lectin Domain from E. coli UTI89 in Complex with Galactoside 5-nitro-2'-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-[1,1'-biphenyl]-3-carboxylic acid


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 290.0
Details 0.1 M Tris 8.0, 0.8 M AmSO4, 10% DSMO

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.12 α = 90
b = 57.12 β = 90
c = 121.29 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CMOS RDI CMOS_8M -- 2018-06-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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
1.39 38.32 99.9 0.088 -- -- 14.2 -- 41077 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.39 1.44 100.0 0.526 -- 5.18 14.2 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.08 38.32 -- 1.33 -- 82908 4137 95.62 -- 0.2007 0.1999 0.217 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.08 1.0923 -- 110 2111 0.3498 0.3395 -- 78.0
X Ray Diffraction 1.0923 1.1051 -- 57 1034 0.3215 0.3716 -- 58.0
X Ray Diffraction 1.1051 1.1186 -- 71 1486 0.3456 0.3882 -- 61.0
X Ray Diffraction 1.1186 1.1328 -- 150 2600 0.3146 0.3204 -- 97.0
X Ray Diffraction 1.1328 1.1477 -- 138 2694 0.2863 0.341 -- 100.0
X Ray Diffraction 1.1477 1.1634 -- 122 2712 0.2743 0.2877 -- 100.0
X Ray Diffraction 1.1634 1.18 -- 155 2674 0.2606 0.2972 -- 100.0
X Ray Diffraction 1.18 1.1976 -- 143 2732 0.2591 0.251 -- 100.0
X Ray Diffraction 1.1976 1.2164 -- 140 2721 0.2518 0.2643 -- 100.0
X Ray Diffraction 1.2164 1.2363 -- 145 2685 0.2491 0.2956 -- 100.0
X Ray Diffraction 1.2363 1.2576 -- 132 2728 0.2528 0.243 -- 100.0
X Ray Diffraction 1.2576 1.2805 -- 146 2724 0.238 0.2302 -- 100.0
X Ray Diffraction 1.2805 1.3051 -- 159 2704 0.2269 0.25 -- 100.0
X Ray Diffraction 1.3051 1.3318 -- 135 2719 0.2179 0.2387 -- 100.0
X Ray Diffraction 1.3318 1.3607 -- 120 2748 0.2179 0.2091 -- 100.0
X Ray Diffraction 1.3607 1.3924 -- 159 2711 0.2055 0.2223 -- 100.0
X Ray Diffraction 1.3924 1.4272 -- 146 2726 0.2067 0.2071 -- 100.0
X Ray Diffraction 1.4272 1.4658 -- 147 2734 0.1968 0.2094 -- 100.0
X Ray Diffraction 1.4658 1.5089 -- 164 2693 0.1903 0.2162 -- 100.0
X Ray Diffraction 1.5089 1.5576 -- 138 2765 0.1859 0.2101 -- 100.0
X Ray Diffraction 1.5576 1.6133 -- 169 2704 0.1814 0.1784 -- 100.0
X Ray Diffraction 1.6133 1.6779 -- 136 2769 0.188 0.2168 -- 100.0
X Ray Diffraction 1.6779 1.7543 -- 141 2744 0.1752 0.1852 -- 100.0
X Ray Diffraction 1.7543 1.8467 -- 139 2780 0.1783 0.1753 -- 100.0
X Ray Diffraction 1.8467 1.9624 -- 155 2766 0.1708 0.1689 -- 100.0
X Ray Diffraction 1.9624 2.114 -- 159 2754 0.1688 0.1813 -- 100.0
X Ray Diffraction 2.114 2.3267 -- 112 2824 0.1748 0.1985 -- 100.0
X Ray Diffraction 2.3267 2.6633 -- 151 2823 0.1914 0.2295 -- 100.0
X Ray Diffraction 2.6633 3.3551 -- 146 2884 0.1905 0.2094 -- 100.0
X Ray Diffraction 3.3551 38.344 -- 152 3022 0.1797 0.205 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_plane_restr 0.005
f_chiral_restr 0.075
f_dihedral_angle_d 16.349
f_angle_d 1.298
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1174
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 225

Software

Software
Software Name Purpose
PHENIX refinement version: 1.8.4_1496
XDS data reduction
XDS data scaling
PHENIX phasing