Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.03317 Å / Relative weight: 1
Reflection
Resolution: 1.57→65.59 Å / Num. obs: 88647 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.14 Å2 Data reduction details: Data were integrated, scaled and merged with the Dials software package using the xia2 pipeline CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.065 / Net I/σ(I): 12.1 / Num. measured all: 601685
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. measured all
Num. unique obs
CC1/2
Rpim(I) all
Rrim(I) all
Net I/σ(I) obs
% possible all
4.26-65.65
6.71
0.032
32034
4774
0.999
0.013
0.034
59.4
99.3
3.38-4.26
7.31
0.035
33483
4583
0.999
0.014
0.038
53.1
100
2.95-3.38
7.51
0.046
34030
4532
0.999
0.018
0.05
34.5
99.9
2.68-2.95
6.37
0.063
28598
4490
0.997
0.027
0.069
21.6
99.4
2.49-2.68
7.02
0.082
31519
4491
0.996
0.033
0.089
15.8
99.6
2.35-2.49
7.21
0.108
32221
4468
0.994
0.043
0.117
11.5
99.8
2.23-2.35
7.3
0.128
32650
4473
0.992
0.051
0.138
9.6
100
2.13-2.23
7.41
0.154
33143
4472
0.989
0.06
0.165
7.5
100
2.05-2.13
7.36
0.199
32642
4438
0.978
0.079
0.214
5.4
100
1.98-2.05
6.2
0.228
27706
4466
0.973
0.098
0.249
4
99.8
1.92-1.98
6.61
0.291
29157
4409
0.964
0.121
0.316
3.1
99.4
1.86-1.92
6.77
0.402
30270
4470
0.939
0.165
0.435
2.2
99.6
1.81-1.86
6.86
0.515
30134
4391
0.918
0.21
0.557
1.6
99.7
1.77-1.81
7.04
0.659
31188
4432
0.903
0.266
0.711
1.3
99.7
1.73-1.77
7.26
0.886
32051
4416
0.826
0.351
0.954
0.9
99.7
1.69-1.73
7.22
1.057
32001
4435
0.785
0.421
1.139
0.7
99.9
1.66-1.69
7.11
1.331
31377
4413
0.706
0.535
1.437
0.6
99.9
1.63-1.66
6.31
1.582
27884
4420
0.673
0.675
1.724
0.4
99.2
1.6-1.63
5.17
1.816
21590
4177
0.464
0.862
2.021
0.3
94.8
1.57-1.6
4.62
2.016
18007
3897
0.377
1.02
2.275
0.3
89
-
Processing
Software
Name
Version
Classification
PHENIX
1.20.1_4487
refinement
PHASER
2.8.3
phasing
DIALS
2.2.10-g6dafd9427-release
datascaling
DIALS
2.2.10-g6dafd9427-release
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→65.59 Å / SU ML: 0.2779 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.2272 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: 1. Hydrogen atoms have been modeled in their riding positions. 2. Mass spectrometry of purified protein shows that Palmitoyl-CoA copurifies with the EspE7-R35A protein during purification ...Details: 1. Hydrogen atoms have been modeled in their riding positions. 2. Mass spectrometry of purified protein shows that Palmitoyl-CoA copurifies with the EspE7-R35A protein during purification when expressed in E.coli. The CoA adduct seen in the electron density maps is disordered to varying degrees in the different pockets in the asymmetric unit. In one pocket, most of the Palmitoyl-CoA can be built with the Adenosine positioned in a less common position relative to other homologs with CoA adducts bound. This is likely due to packing constraints. In some symmetry copies, there is considerable disorder of the region beyond the diphosphate and the Adenosine was left unmodeled with some difference peaks that likely represent its multiple positions. Along the fatty acid chain, the density gets weaker as one goes further from the CoA and deeper into the binding pocket. Most chains have good density to around the C8-C10 position with not much density beyond C12. Building full length Palmitoyl tail in the pocket results in negative difference density for the terminal atoms. There is also clear disorder for the side-chain of Met-91 with one conformer blocking longer chain fatty acids in the pocket. In the end, the ligand was modeled as dodecyl-CoA (lauryl-CoA). The presumption is that there could be a mix of fatty acid chain lengths of coA adducts bound and co-purified. 3. The metal ion near the fatty acid chain was modeled as a potassium ion. The presence of an anomalous peak similar in height to sulfur atoms suggests it is heavier than Na or Mg. The height of this anomalous peak is unchanged when the data was re-collected above and below the Zn K-edge and below the iron K-edge, suggesting that the metal must be lighter than Fe. The lack of a signal for Mn in an X-ray fluorescence emission spectra suggests it is not Mn. The two most likely candidates from the anomalous and X-ray fluorescence experiments is Calcium and Potassium - both of which would have anomalous peaks at the energies used for data collection (12000, 9709, 9609 and 7000 eV) and also emit at an energy below where the beamline setup can detect in the emission spectra. Looking at the results of the geometric and valence sum criteria when modeled as Ca and K on the check my metal server, both options had several criteria that were supportive of the assignment and some that were marginal. In the end, K was selected as being slightly more favorable but the assignment is not definitive. 4. There are a large number of residues at the N- and C-termini that cannot be built due to disorder. The C-terminal region was predicted to be disordered. An extra 10 residues from chain B can be built as they are packed against a symmetry adjacent tetramer. In chain D, density for the C-terminus packing against a neighboring tetramer is also visible, but it is not ordered enough to reliably build. The N-terminal expression and purification tag cannot be built. There are a number of un-built difference map peaks along the surface of the protein that are likely protein residues from the C-terminus or N-terminus of symmetry adjacent tetramers, but it was not possible to build and identify the register of these residues.
Rfactor
Num. reflection
% reflection
Rfree
0.2035
4178
4.84 %
Rwork
0.1775
82233
-
obs
0.1788
86411
96.53 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL