Table 1.
Data collection and refinement statistics
| PvdPapo | PvdPTyr | PvdPSeMet | |
|---|---|---|---|
| Data collection statistics | |||
| Beamline | PETRAIII P11 | BESSYII 14.2 | SLS X06DA/PETRAIII P11 |
| No. of crystals | 1 | 1 | 3 |
| Wavelength (Å) | 0.9794 | 1.282 | 0.9779/0.9794 |
| Space group | P21 | P21 | P21 |
| Unit cell dimensions | |||
| a, b, c (Å) | 97.35, 107.79, 107.94 | 77.33, 109.14, 82.51 | 96.19, 108.41, 108.41 |
| α, β, γ (°) | 90, 99.97, 90 | 90, 95.55, 90 | 90, 99.70, 90 |
| Resolution range (Å) (highest shell) | 48.07–2.09 (2.26–2.09) | 48.09–2.70 (3.03–2.70) | 48.34–3.50 (3.70–3.50) |
| Ellipsoidala resolution (Å) (direction)b | 2.84 (0.988 a* − 0.152 c*) | 3.73 (0.718 a* − 0.696 c*) | n.a.c |
| 2.19 (b*) | 2.7 (b*) | n.a. | |
| 2.09 (−0.032 a* + 0.999 c*) | 2.93 (0.64 a* + 0.768 c*) | n.a. | |
| Total no. of reflections (ellipsoidal)d | 578,302 (27,712) | 229,383 (8,710) | 2,663,558 (404,486) |
| No. of unique reflections (ellipsoidala)d | 85,942 (4,285) | 23,084 (1,154) | 54,434 (8,374) |
| Average multiplicityd | 6.7 (6.5) | 9.9 (7.5) | 48.9 (48.3) |
| Completenessd (%) | 66.3 (16.0) | 61.5 (10.5) | 99.9 (100.0) |
| Completeness (ellipsoidala)d,e (%) | 93.2 (76.7) | 92.1 (56.5) | n.a. |
| I/σ(I) (ellipsoidala)d | 10.7 (1.6) | 8.6 (1.6) | 18.1 (10.6) (spherical) |
| Rmeasd,f | 0.13 (1.28) | 0.32 (1.49) | 0.27 (0.54) |
| Rpimd,g | 0.051 (0.50) | 0.10 (0.54) | NDh |
| CC½i | 0.99 (0.54) | 0.99 (0.51) | 0.99 (0.99) |
| Refinement statistics | |||
| Resolution (Å) | 45.61–2.09 | 48.09–2.70 | |
| No. of reflections used | 85,901 | 22,962 | |
| Rworkj (%) | 21.41 | 20.46 | |
| Rfreek (%) | 24.10 | 26.18 | |
| No. of residues | |||
| Protein | 1,889 | 916 | |
| Water | 513 | 24 | |
| Zn2+ | 4 | ||
| l-Tyrosine | 2 | ||
| Mean B-factorl (Å2) | 48 | 34 | |
| All protein residues | 48 | 34 | |
| Ligands | 36 | ||
| Water molecules | 38 | 20 | |
| r.m.s.d. | |||
| Bond length (Å)m | 0.002 | 0.002 | |
| Bond angle (°)m | 0.495 | 0.460 | |
| Ramachandran plot (%) | |||
| Favored regionsm | 96.82 | 96.6 | |
| Allowed regionsm | 100 | 100 | |
| Outliersm | 0 | 0 | |
| MolProbity scorem | 1.00 | 0.95 | |
| PDB code | 6EYS | 6EYV | |
a Statistics refer to data truncated by STARANISO to remove weak reflections affected by anisotropy (46).
b The resolution limits for three directions in reciprocal space (a*, b*, c*) are indicated here. To accomplish this, STARANISO computed an ellipsoid postfitted by least squares to the cutoff surface, removing points where the fit was poor. Note that the cutoff surface is unlikely to be perfectly ellipsoidal, so this is only an estimate.
c n.a., not applicable.
d Values in parentheses are for the highest-resolution shell.
e The anisotropic completeness was obtained by least squares fitting an ellipsoid to the reciprocal lattice points at the cutoff surface defined by a local mean I/σ(I) threshold of 1.5, rejecting outliers in the fit due to spurious deviations (including any cusp) and calculating the fraction of observed data lying inside the ellipsoid so defined. Note that the cutoff surface is unlikely to be perfectly ellipsoidal, so this is only an estimate.
f Rmeas = Σhkl{N(hkl)/[N(hkl) − 1]}1/2 × Σi|Ii(hkl) − 〈I(hkl)〉|/ΣhklΣi Ii(hkl).
g Rpim = Σhkl{1/[N(hkl) − 1]}1/2 × Σi|Ii(hkl) − 〈I(hkl)〉|/ΣhklΣiIi(hkl).
h Not determined.
i CC1/2 = Σ(x − 〈x〉)(y − 〈x〉)/[Σ(x − 〈x〉)2Σ(y − 〈y〉)2]1/2.
j Rwork = (Σhkl‖Fobs| − k|Fcalc‖)/(Σhkl|Fobs|).
k Rfree is the same as Rwork with 5% of reflections chosen at random and omitted from refinement.
l B-factors calculated with Moleman2 (55).
m Statistics calculated with the MolProbity web server (56) (http://molprobity.biochem.duke.edu/) (Please note that the JBC is not responsible for the long-term archiving and maintenance of this site or any other third party-hosted site.).