Table 1. LptDE data collection and refinement statistics.
Yersinia
LptDE |
Klebsiella
LptDE |
Full-length
Klebsiella LptDE |
Pseudomonas
LptDE |
|
---|---|---|---|---|
Data Collection | ||||
wavelength (Å) | 1.0 | 1.0 | 1.0 | 1.0 |
Space Group | P21 | P21 | I222 | C2221 |
Mol/ASU‡ | 4 | 2 | 1 | 1 |
X-ray source | APS-22-ID | APS-22-ID | APS 23-ID-D | APS 23-ID-B |
a, b, c (Å) | 82.8, 176.3, 143.8 |
75.2, 173.0, 84.0 | 130.6, 154.9, 194.9 |
149.1, 156.1, 115.8 |
α, β, γ (°) | 90, 96.1, 90 | 90, 111.3, 90 | 90, 90, 90 | 90, 90, 90 |
dmin (Å)* | 2.75 (2.85-2.75) | 2.95 (3.06-2.95) | 4.45 (4.57-4.45) | 3.00 (3.11-3.00) |
Completeness (%)* | 99.3 (95.1) | 97.4 (95.1) | 95.6 (94.7) | 100.0 (100.0) |
Redundancy* | 3.6 (3.4) | 4.0 (3.8) | 5.5 (4.9) | 7.2 (7.1) |
Rmerge †* | 0.159 (0.786) | 0.067 (0.999) | 0.099 (0.848) | 0.132 (0.999) |
I/σ (I)* | 8.4 (1.48) | 16.6 (1.34) | 14.3 (1.8) | 12.4 (1.25) |
Refinement | ||||
Resolution | 40.1-2.75 | 41.4-2.95 | 44.7-4.36 | 49.0-2.98 |
Reflections | 106218 | 41834 | 10921 | 27493 |
Atoms | 22831 | 11347 | 7275 | 6104 |
Amino acids | 2740 | 1566 | 908 | 731 |
Rwork§/Rfree¶ | 0.21/0.26 | 0.23/0.28 | 0.30/0.34 | 0.24/0.29 |
PDB code | 5IXM | 5IV8 | 5IV9 | 5IVA |
Validation | ||||
Average B-factor (Å2) | 47.0 | 72.6 | 97.1 | 81.2 |
Bond angle RMSD (°) | 0.998 | 0.488 | 0.631 | 0.668 |
Bond length RMSD (Å) | 0.004 | 0.002 | 0.003 | 0.003 |
Ramachandran favored (%)¥ | 91.5 | 93.5 | 86.8 | 92.5 |
Ramachandran allowed (%)¥ | 6.2 | 5.9 | 10.1 | 6.8 |
Clashscore | 9.7 | 2.7 | 5.4 | 7.2 |
Copies of the LptDE complex per asymmetric unit.
Indicates statistics for last resolution shell shown in parenthesis.
Rmerge = Σhkl,j (|Ihkl-<Ihkl>|) / Σhkl,j Ihkl, where <Ihkl> is the average intensity for a set of j symmetry related reflections and Ihkl is the value of the intensity for a single reflection within a set of symmetry-related reflections.
Rwork = Σhkl (||Fo| - |Fc||) / Σhkl|Fo| where Fo is the observed structure factor amplitude and Fc is the calculated structure factor amplitude.
Rfree = Σhkl,T(||Fo| - |Fc||) / Σhkl,T|Fo|, where a test set, T, is omitted from the refinement.
Calculated with Molprobity.