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. 2021 Feb 25;296:100463. doi: 10.1016/j.jbc.2021.100463

Table 2.

X-ray data collection statistics and model refinement statistics

X-ray data and model parameters Pcryo_0638 Pcryo_0637 UDP/acetyl-CoA Pcryo_0637 CoA/UDP-2,4-diacetamido-2,4,6-trideoxy-d-glucose Pcryo_0637 CoA/UDP-2-acetamido-4-amino-2,4,6-trideoxy-d-glucose Pcryo_0637 tetrahedral intermediate
Resolution limits (Å) 50.0–1.30 (1.40–1.30)a 50.0–1.30 (1.40–1.30)a 50.0–1.55 (1.65–1.55)a 50.0–1.30 (1.40–1.30)a 50.0–1.40 (1.50–1.40)a
Number of independent reflections 202026 (36,011) 56,307 (11,060) 33,312 (5566) 56,136 (10,804) 45,470 (8481)
Completeness (%) 92.9 (83.0) 98.2 (96.6) 98.1 (95.0) 98.3 (94.6) 98.8 (97.9)
Redundancy 2.4 (1.9) 6.1 (2.8) 5.1 (2.4) 8.1 (2.5) 5.9 (3.3)
avg I/avg σ(I) 7.2 (1.9) 17.6 (3.0) 19.6 (3.0) 20.3 (2.4) 20.2 (3.3)
Rsym (%)b 5.7 (22.9) 6.2 (43.6) 4.5 (34.1) 5.4 (44.8) 4.9 (38.0)
cR-factor (overall)%/no. reflections 15.1/202026 19.5/56,307 16.4/33,312 17.7/56,136 15.9/45,470
R-factor (working)%/no. reflections 15.0/191942 19.4/53,390 16.2/31,600 17.3/53,279 15.8/43,279
R-factor (free)%/no. reflections 16.9/10,084 21.4/2917 19.0/1712 19.4/2857 18.2/2191
Number of protein atoms 6354 1642 1635 1649 1651
Number of heteroatoms 1480 364 355 373 379
Average B values
 Protein atoms (Å2) 12.2 11.8 17.8 14.7 14.5
 Ligand (Å2) 10.2 18.6 34.1 24.6 23.4
 Solvent (Å2) 28.1 26.6 33.5 29.5 30.1
Weighted RMS deviations from ideality
 Bond lengths (Å) 0.010 0.010 0.009 0.010 0.010
 Bond angles (°) 1.55 1.90 1.60 1.60 1.70
 Planar groups (Å) 0.009 0.008 0.008 0.008 0.009
Ramachandran regions (%)d
 Most favored 98.6 94.9 95.8 96.3 95.8
 Additionally allowed 1.4 5.1 4.2 3.7 4.2
 Generously allowed 0.0 0.0 0.0 0.0 0.0
 PDB code 7L7X 7L7Y 7L7Z 7L81 7L82
a

Statistics for the highest resolution bin.

b

Rsym=(|II¯|/I)×100.

c

R-factor = (Σ|Fo - Fc|/Σ|Fo|) x 100 where Fo is the observed structure-factor amplitude and Fc is the calculated structure-factor amplitude.

d

Distribution of Ramachandran angles according to PROCHECK (26).