Table 1. Statistics of X-ray diffraction data, phasing and structure refinement.
Data set | Native | Mercury derivative |
Wavelength (Å) | 1.095 | 1.095 |
Space group | P21212 | P21212 |
Cell dimensions (Å) | a = 93.4, b = 99.7, c = 45.3 | a = 93.0, b = 99.9, c = 45.2 |
Resolution (Å) | 34.0–2.38 (2.47–2.38) | 34.0–2.40 (2.49–2.40) |
Unique reflections | 17129 (1662) | 15356 (1444) |
Multiplicity | 2.7 (2.6) | 8.6 (8.5) |
Completeness (%) | 96.9 (97.0) | 86.3 (83.4) |
<I/σ(I)> | 11.94 (2.2) | 22.45 (3.91) |
Rsym a (%) | 3.8 (30.8) | 5.6 (41.0) |
Phasing statistics | ||
Heavy atom sites | 2 x Hg | |
Resolution (Å) | 34–4.0 (34–3.0) | |
Figure of merit (acentric/centric) | 0.36/0.28 (0.18/0.17) | |
bPhasing power (iso/ano) | 0.99/1.27 (0.72/0.91) | |
c Rcullis (iso/ano) | 0.82/0.75 (0.89/0.85) | |
Refinement statistics | ||
Molecules (ASU) | 2 | |
No. of protein atoms | 2267 | |
No. of waters | 90 | |
Average B-factor (Å2) (protein/water) | 53.6/53.4 | |
Rwork d (%) | 21.1 | |
Rfree d (%) | 25.4 | |
Rms deviation | ||
Bond length (Å) | 0.006 | |
Bond angle (°) | 0.93 | |
Coordinate error (maximum-likelihood based) | 1.61 | |
Ramachandran plot | ||
Res. in most favored regions (%) | 86.2 | |
Res. in additional allowed regions (%) | 13 | |
Res. in generously allowed regions (%) | 0.8 |
Numbers in parenthesis refer to the highest resolution shell (2.47–2.38 Å).
Rsym = ∑hkl(∑i[|Ihkl, i − <Ihkl>|]) / ∑hkl, i<Ihkl>, where Ihkl, I is the intensity of an individual measurement of the reflection with Miller indices h, k, and l, and <Ihkl> is the mean intensity of that reflection.
Phasing power = < phase-integrated lack of closure >/< FPH – FP>, where FPH is the structure factor of the heavy atom derivative and FP is the structure factor of the native protein.
Rcullis = <[|FH, calc|/ phase-integrated lack of closure]>, where FH, calc is the calculated structure factor for the heavy atom.
Rwork = ∑hkl(||Fo, hkl| − |Fc, hkl||) / |Fo, hkl|, where |Fo, hkl| and |Fc, hkl| are the observed and calculated structure factor amplitudes. Rfree is defined and calculated in an equivalent manner, but based on a subset of 5% randomly selected reflections.