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. Author manuscript; available in PMC: 2017 Jun 7.
Published in final edited form as: Structure. 2016 May 5;24(6):965–976. doi: 10.1016/j.str.2016.03.026

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.