TABLE 2.
Summary of x-ray data and model parameters for S. coelicolor GlgE isoform 1 complexes
Values in parentheses are for the outer resolution shell. r.m.s., root mean square; —, no other ligands.
| Data set | E423A + maltoheptaose | E423A + malto-octaose | D394A + maltodextrin |
|---|---|---|---|
| Data collection | |||
| Beamline | I04-1 | I04-1 | I24 |
| Wavelength (Å) | 0.920 | 0.920 | 0.978 |
| Detector | Pilatus 2 m | Pilatus 2 m | Pilatus 6 m |
| Resolution range (Å) | 62.83–2.30 (2.36–2.30) | 49.92–2.50 (2.56–2.50) | 81.40–1.95 (2.00–1.95) |
| Space group | P41212 | P41212 | P41212 |
| Cell parameters (Å) | a = b = 114.08, c = 314.14 | a = b = 113.61, c = 313.69 | a = b = 115.11, c = 311.36 |
| Total no. of measured intensities | 1,708,887 (119,311) | 938,920 (42,909) | 1,934,155 (27,203) |
| Unique reflections | 92,902 (6,680) | 72,101 (5,252) | 147,828 (8,730) |
| Multiplicity | 18.4 (17.9) | 13.0 (8.2) | 13.1 (3.1) |
| Mean I/σ(I) | 27.6 (3.5) | 17.9 (2.3) | 17.5 (1.2) |
| Completeness (%) | 99.9 (99.4) | 100.0 (100.0) | 97.1 (79.9) |
| Rmergea | 0.068 (0.998) | 0.091 (0.846) | 0.083 (0.837) |
| Rmeasb | 0.071 (1.056) | 0.098 (0.967) | 0.086 (1.081) |
| CC1/2c | 0.999 (0.868) | 0.999 (0.628) | 0.999 (0.589) |
| Wilson B value (Å2) | 47.0 | 50.9 | 26.1 |
| Refinement | |||
| Resolution range (Å) | 62.83–2.30 (2.36–2.30) | 49.92–2.50 (2.56–2.50) | 81.40–1.95 (2.00–1.95) |
| Reflections: working/freed | 88,145/4,636 | 68,441/3,560 | 140,419/7,409 |
| Rwork/Rfreee | 0.181/0.209 (0.252/0.272) | 0.179/0.209 (0.314/0.361) | 0.177/0.194 (0.349/0.365) |
| Ramachandran plot: favored/allowed/disallowedf (%) | 98.5/1.3/0.2 | 97.8/2.1/0.1 | 98.1/1.6/0.3 |
| r.m.s. bond distance deviation (Å) | 0.011 | 0.010 | 0.010 |
| r.m.s. bond angle deviation (°) | 1.44 | 1.43 | 1.40 |
| No. of protein residues: chain A/chain B (ranges) | 649 (15–663)/649 (15–663) | 649 (15–663)/649 (15–663) | 648 (15–662)/648 (15–662) |
| No. of sugars/water molecules/other ligands | 24/484/0 | 26/447/0 | 29/1,092/5 |
| Mean B factors: protein/sugars/water/other/overall (Å2) | 61/80/53/—/61 | 67/93/54/—/67 | 34/56/37/62/35 |
| Protein Data Bank accession code | 5CVS | 5LGV | 5LGW |
a Rmerge = ΣhklΣi|Ii(hkl) − 〈I(hkl)〉|/ΣhklΣiIi(hkl).
b Rmeas = Σhkl[N/(N − 1)]1/2 × Σi|Ii(hkl) − 〈I(hkl)〉|/ΣhklΣiIi(hkl) where Ii(hkl) is the ith observation of reflection hkl, 〈I(hkl)〉 is the weighted average intensity for all observations i of reflection hkl, and N is the number of observations of reflection hkl.
c CC1/2 is the correlation coefficient between symmetry-equivalent intensities from random halves of the data set.
d The data set was split into “working” and “free” sets consisting of 95 and 5% of the data, respectively. The free set was not used for refinement.
e The R factors Rwork and Rfree were calculated as follows: R = Σ(|Fobs − Fcalc|)/Σ|Fobs| where Fobs and Fcalc are the observed and calculated structure factor amplitudes, respectively.
f As calculated using MolProbity (43).