Structure of the month - January 2005

Kuper_January05_fig1

Figure 1. The structure of Cnx1G-MPT (a, substrate) and S583A-MPT-AMP (b, product) complexes. Ribbon representation of Cnx1G (a) and S583A (b). Green and orange colouring indicates helices and β-strands. Bound MPT and MPT-AMP are shown in ball-stick-mode covered by the 2Fo-Fc electron density contoured at 1.0 sigma. Difference density (Fo-Fc) is shown in red (3.5 sigma).


Kuper_January05_fig2

Figure 2. Cu-MPT dithiolate complex. a, Fluorescence scan of Cnx1G crystal at the Cu absorption edge. b, Anomalous Fourier maps (coloured) from diffraction data recorded at 1.05 Å (blue, 5.0 sigma) and 1.75 Å (yellow, 3.0 sigma) of S583A surrounding the Cu-site and 2Fo-Fc maps (grey) for non-dithiolate ligands. Dashed lines indicate bonds between Cu and coordinating atoms.


Data collection

 
Data set*I* WT-1 WT-2 WT-3 WT-4 S583A-1 S583A-2
Wavelength (Å) 1.050 1.377 1.385 1.750 1.050 1.750
Max. Resolution (Å) 1.60 1.90 1.90 1.85 1.45 1.80
Completeness*II* 99.9 (100) 99.6 (99.6) 97.6 (97.6) 100 (100) 99.3 (99.9) 97.0 (97.0)
Completenessano*II* 99.8 (100) 99.8 (100) 97.3 (99.7) 99.8 (99.8) 99.9 (100) 94.6 (90.8)
Mean Redundancy 7.7 (7.6) 8.0 (8.0) 8.1 (7.9) 7.5 (7.3) 6.9 (6.7) 5.6 (5.6)
Rsym*II**III* 5.7 (39.0) 6.5 (29.6) 9.0 (53.0) 6.0 (36.8) 5.5 (40.0) 6.6 (45.8)
I/sigI*II**IV* 7.6 (1.9) 9.2 (2.4) 6.5 (1.3) 7.8 (1.8) 6.3 (1.8) 9.0 (1.8)
Number of reflections 28748 17573 16897 18910 36739 19640

Refinement

 
Data set WT-1 S583A-1
Resolution limits (Å) 20-1.6 27-1.45
Number of reflections 27323 36122
Number of protein / solvent atoms 1216 / 155 1215 / 168
Rcryst / Rfree (%)*V* 16.5 / 19.1 16.3 / 17.9
Deviations from ideal values in
   Bond distances (Å)
   Angles (°)
   Torsion angles (°)
   Chiral-center restraints (Å3)
   Plane restraints (Å)
 
0.014
1.509
4.972
0.198
0.006
 
0.012
1.450
4.850
0.184
0.005
Ramachandran statistics 93.4/6.6/0/0 94.1/5.9/0/0

Table. Data collection and refinement statistics.
*I* All crystals belong to space group F4132 (a=b=c=171.1 Å).
*II* Numbers in parentheses correspond to the highest resolution shell.
*III* Rsym = ∑hkli |Ii - | / ∑hkli Ii where Ii is the ith measurement and is the weighted mean of all measurements of I.
*IV* / indicates the average of the intensity divided by its average standard deviation.
*V* Rcryst=∑hkl||Fo|-|Fc||/∑hkl|Fo| where Fo and Fc are the observed and calculated structure factor amplitudes. Rfree same as Rcryst for 5% of the data randomly omitted from refinement. The number of reflections includes the Rfree subset. Ramachandran statistics indicate the fraction of residues in the most favored, additionally allowed, generously allowed, and disallowed regions of the Ramachandran diagram as defined by PROCHECK [Laskowski, R. A., et al. J. Mol. Biol. 231, 1049-67 (1993)].