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Figure 2
Correlation of solvent-flattened phases with true phases [〈cos(Δφ)〉] for model data in a unit cell containing 70% solvent as a function of resolution. Structure factors (6906 model data from ∞ to 3.0 Å) were generated based on coordinates from a dehalogenase enzyme from Rhodococcus species ATCC 55388 (American Type Culture Collection, 1992BB31) determined recently in our laboratory (J. Newman, personal communication), except that only the N-terminal 174 residues (of 267) were included in the calculation in order to simulate a unit cell with 70% solvent. The calculation was performed in space group P21212 with unit-cell dimensions a = 94, b = 80, c = 43 Å and one molecule in the asymmetric unit. Electron density for the solvent region was introduced by calculating a model electron-density map based on protein atoms alone, setting the mean electron density in the solvent region (greater than 2.5 Å from any protein atom) to 0.32 e Å−3 and the mean electron density in the protein region to 0.43 e Å−3, respectively, smoothing the interface between solvent and protein region to minimize the introduction of high-frequency terms and calculating an inverse Fourier transform to obtain model phases and amplitudes. Phases with simulated errors were generated by adding phase errors with a distribution given by P(Δφ) = exp[Acos(Δφ) + Ccos2(Δφ)], with the values A = 0.8 and C = 0.4 for acentric reflections and A = 0.4 and C = 0.2 for centric reflections. This led to an average value of the cosine of the phase error (i.e. the true figure of merit of the phasing) of 〈cos(Δφ)〉 = 0.42 for acentric and 0.39 for centric reflections. The model data with simulated errors was then solvent flattened by the reciprocal-space method as described here and by the real-space method as implemented in the program dm (Cowtan & Main, 1996BB6), version 1.8, using solvent flattening and omit mode. Although dm will carry out solvent flattening alone in this way, it should be noted that this is a non-recommended mode (all recommended modes also contain histogram matching, which we did not include in order to keep the comparison restricted to the use of solvent flattening). Circles, starting phases; squares, real-space solvent flattening; diamonds, reciprocal-space solvent flattening.

Journal logoBIOLOGICAL
ISSN: 1399-0047
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