Table I. Crystallographic data collection and structure refinement statistics for A.aeolicus Trbp111 and its E.coli homolog.
| Crystal |
E.coli homolog |
|
|
|
|
A.aeolicus Trbp111 |
|---|---|---|---|---|---|---|
| Native | Hg acetate | PtK2Cl4 | TMPbAca | 3-wavelength Pt derivative | ||
| Space group | P3221 | C2 | ||||
| Unit cell a, c (Å) | 41.2, 95.3 | 41.3, 95.2 | 40.9, 95.3 | 41.3, 95.6 | 41.6, 96.2 | 145.4,72.79 (b), 68.94,β = 91.93° |
| Wavelength (Å) | 1.54 | 1.54 | 1.54 | 1.54 | 1.074, 1.0733, 1.055 | 1.08 |
| Resolution (Å) | 1.87 | 2.3 | 2.8 | 2.0 | 1.9 | 2.4 |
| last bin (Å) | 1.94–1.87 | 2.38–2.3 | 2.85–2.8 | 2.07–2.0 | 1.93–1.9 | 2.44–2.40 |
| Unique reflections | 8064 | 4466 | 2514 | 6791 | 8024, 8032, 8478 | 26611 |
| Completeness (%) | 97.4 | 95.3 | 99.8 | 99.6 | 99.2, 99.3, 99.2 | 94.0 |
| last bin | 96.1 | 80.5 | 100.0 | 100.0 | 100.0, 100.0, 98.9 | 88.4 |
| Rsym (%)b | 3.1 | 3.0 | 9.9 | 3.9 | 6.6, 6.3, 6.2 | 4.2 |
| last bin | 11.6 | 8.3 | 36.1 | 10.2 | 32.9, 35.7, 45.2 | 36.1 |
| <I/σ(I)> | 19.0 | 15.8 | 5.8 | 20.6 | 12.0, 11.5, 10.9 | 9.7 |
| last bin | 13.6 | 7.2 | 3.2 | 15.6 | 5.9, 6.3, 4.5 | 2.9 |
| Final phasing statistics (7.0–2.0 Å) | (35–2.0 Å) | |||||
| Rder (%)c | 12.3 | 29.7 | 10.1 | 1.9, 2.9d | ||
| Ranom (%)e | 3.9 | 6.8 | 2.0 | 3.6, 3.7d | ||
| Rcullisf | 0.82 | 0.81 | 0.71 | 0.65, 0.73d | ||
| number of sites | 2 | 2 | 1 | 2 | ||
| phasing powerg | ||||||
| isomorphous | 0.96 | 1.35 | 1.15 | 1.1, 1.1d | ||
| anomalous | 0.65 | 1.2 | 0.80 | 2.6, 2.6d | ||
| FOMh (overall, 20–2.0 Å) | 0.54 | 0.32 | ||||
| FOM after density modification (20–1.87 Å) | 0.95 | |||||
| Refinement statistics | ||||||
| resolution range (Å) | 20–1.87 | 20–2.5 | ||||
| no. of reflectionsi | 7989 | 23 601 | ||||
| no. of non-H atoms | ||||||
| protein | 860 | 3216 | ||||
| water | 136 | 141 | ||||
| r.m.s.d. bond length (Å) | 0.007 | 0.005 | ||||
| r.m.s.d. bond angle (°) | 1.73 | 1.6 | ||||
| R-cryst (%)j, F > 0 | 15.8 | 18.9 | ||||
| R-free (%)k, F > 0 | 19.8 | 22.0 | ||||
| Ramachandran plot (%)l | ||||||
| favored | 96.1 | 89.9, 90.0, 90.2, 89.0 | ||||
| allowed | 3.9 | 10.1, 10.0, 9.8, 11.0 | ||||
| mean b-factor for protein atoms (Å3/Da) | 20.0 | 26.8 |
aTMPbAc, trimethyl lead acetate.
bRsym = 100 × (∑h∑i|<I(h)> – I(h)i|) ÷ ∑h∑iI(h)i, where I(h)i is the ith measurement of reflection h and <I(h)> is the mean intensity of the n symmetry-related measurements.
cRder = 100 × (∑h|FPH – FP|) ÷ ∑h|FP|, where FP and FPH are the observed structure factor amplitudes of the native and the derivative, respectively.
dFor MAD data, the dispersive differences were treated as isomorphous replacement information where the data collected at wavelength 1.074 Å are treated as native data (Terwilliger, 1994).
eRanom = 100 × (∑h|FPH+ – FPH–|) ÷ ∑h|<FPH>|, where FPH+ and FPH– are the Friedel pair observed structure factor amplitudes of the derivative at a given wavelength and <FPH> is their average.
fRCullis = ∑h[|FH| – (|FPH| – |FP|)] ÷ ∑h(|FPH| – |FP|), where |FH| is the calculated heavy atom structure factor for reflection h.
gPPiso = (1/Nrefl)∑h[||FPH| – |FP|| ÷ <_UNICODE:8747>02π(|FPH – FPHcalc|)P(ϕ)d(ϕ) ], where P(ϕ) is the probability of a phase value of ϕ for reflection h. PPano = (1/Nrefl) ∑h[|ΔobsANO| ÷ <_UNICODE:8747>02π(|ΔobsANO – ΔcalcANO|)P(ϕ)d(ϕ), where ΔobsANO and ΔcalcANO are the Friedel pair differences in the observed and calculated structure factor amplitudes, respectively, for reflection h.
hFOM, figure of merit.
iReflections with F > 0 were used in refinement.
jCrystallographic R factor = 100 × [∑h||Fobs(h)| – |Fcalc(h)||] ÷ ∑h|Fobs(h)|, where Fobs(h) and Fcalc(h) are the observed structure factor amplitude and the structure factor amplitude calculated from the model, respectively.
kThe free R-factor was calculated using 90% of the data in the last round of refinement.
lThe Ramachandran plot was generated in PROCHECK (Howard et al., 1987).