Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.45 mM EF-Tu in 50 mM Tris, pH 7.8, 10 mM GDP, 10 mM magnesium chloride, 0.5% PEG 3350, 5.5 mM ammonium acetate, 2.7 mM ammonium citrate, 1.34 mM ChemDiv compound 1013-0135, VAPOR ...Details: 0.45 mM EF-Tu in 50 mM Tris, pH 7.8, 10 mM GDP, 10 mM magnesium chloride, 0.5% PEG 3350, 5.5 mM ammonium acetate, 2.7 mM ammonium citrate, 1.34 mM ChemDiv compound 1013-0135, VAPOR DIFFUSION, SITTING DROP, temperature 293K
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Data collection
Diffraction
Mean temperature: 95 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.033 Å
Resolution: 3.4→60.232 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Used CNS specialized task files for refinement with hemihedrally twinned data. Twin operator was (-h,-k,l), and twin fraction was 0.294. R-factors reported are the twinned R-factors from CNS. ...Details: Used CNS specialized task files for refinement with hemihedrally twinned data. Twin operator was (-h,-k,l), and twin fraction was 0.294. R-factors reported are the twinned R-factors from CNS. (R-factors after detwinning: R-work=0.2867, R-free=0.3267)
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2619
586
8.4 %
Used CNS task file make_cv_twin.inp to select cross-validation set such that pairs of twin-related reflections were designated to be in the same set, either the working set or the test set.
Rwork
0.197
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-
-
all
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6987
-
-
obs
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6083
87.1 %
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Solvent computation
Bsol: 73.771 Å2
Displacement parameters
Biso mean: 75.7 Å2
Baniso -1
Baniso -2
Baniso -3
1-
8.819 Å2
2.011 Å2
0 Å2
2-
-
8.819 Å2
0 Å2
3-
-
-
-17.639 Å2
Refinement step
Cycle: LAST / Resolution: 3.4→60.232 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2981
0
29
4
3014
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.0114
X-RAY DIFFRACTION
c_angle_deg
1.73
X-RAY DIFFRACTION
c_dihedral_angle_d
24.688
X-RAY DIFFRACTION
c_improper_angle_d
1.184
Xplor file
Refine-ID
Serial no
Param file
X-RAY DIFFRACTION
1
CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION
2
MYTOPPAR:gdp_cns4.param
X-RAY DIFFRACTION
3
CNS_TOPPAR:ion.param
X-RAY DIFFRACTION
4
CNS_TOPPAR:water_rep.param
+
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