 | Acta Crystallographica Section D Acta Crystallographica Section D BIOLOGICAL CRYSTALLOGRAPHY |
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![[Figure 5]](ea5095fig5mag.jpg)
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Figure 5
Comparison of quality of density-modified maps obtained using the skewness of electron density and correlation of local r.m.s. density for scoring with those obtained using the true map quality (correlation to the corresponding model map) for scoring. See text for details. The light blue bars labeled `Perfect scoring' correspond to running the PHENIX AutoSol wizard and using the actual experimental map quality to make decisions at each step prior to obtaining density-modified phases and using the actual density-modified map quality to make the final choice of solution. The dark maroon bars labeled `Bayesian scoring' correspond to using the Bayesian scores for experimental maps based on the skewness of electron density and correlation of local r.m.s. density and using the model–map correlation to choose the final density-modified solution. The light green bars labeled `Random scoring' correspond to using random scores to make decisions about experimental map quality and model–map correlation to choose the final solution. Each `random scoring' value is the average of ten separate runs of PHENIX AutoSol wizard carried out with differing random seeds. Note that the `perfect scoring' method does not necessarily lead to the best final map. For example, an experimental map that is not the best one but is chosen by another scoring method could adventitiously yield additional sites that lead to a better final solution. (a) Structures determined using MAD. Structures shown are aep-transaminase (PDB code 1m32; Chen et al., 2002  ), armadillo (3bct; Huber et al., 1997), cobd (1kus; Cheong et al., 2002), cp-synthase (1l1e; Huang et al., 2002), cyanase (1dw9; Walsh et al., 2000), epsin (1edu; Hyman et al., 2000), gene-5 (1vqb; Skinner et al., 1994), gere (1fse; Ducros et al., 2001), gpatase (1ecf; Muchmore et al., 1998), group2-intron (1kxk; Zhang & Doudna, 2002), ic-lyase (1f61; Sharma et al., 2000), lysozyme (unpublished results; CSHL Macromolecular Crystallography Course), mbp (1ytt; Burling et al., 1996), mev-kinase (1kkh; Yang et al., 2002), nsf-d2 (1nsf; Yu et al., 1998), p32 (1p32; Jiang et al., 1999), p9 (1bkb; Peat et al., 1998), pdz (1kwa; Daniels et al., 1998), psd-95 (1jxm; Tavares et al., 2001), rab3a (1zbd; Ostermeier & Brunger, 1999), s-hydrolase (1a7a; Turner et al., 1998), synapsin (1auv; Esser et al., 1998), tryparedoxin (1qk8; Alphey et al., 1999) and vmp (1l8w; Eicken et al., 2002) (b) Structures determined using SAD: 1029B (1n0e; Chen et al., 2004), 1038B (1lql; Choi et al., 2003), 1063B (1lfp; Shin et al., 2002), 1071B (1nf2; Shin, Roberts et al., 2003), 1102B (1l2f; Shin, Nguyen et al., 2003), 1167B (1s12; Shin et al., 2005), rnase-p (1nz0; Kazantsev et al., 2003), calmodulin (1exr; Wilson & Brunger, 2000), fusion-complex (1sfc; Sutton et al., 1998), insulin (2bn3; Nanao et al., 2005), myoglobin (A. Gonzales, personal communication), nsf-n (1qcs; Yu et al., 1999), sec17 (1qqe; Rice & Brunger, 1999) and ut-synthase (1e8c; Gordon et al., 2001). Note that fusion-complex was solved with SAD plus SIR. (c) Structures determined using MIR: flr (1bkj; Tanner et al., 1996), granulocyte (2gmf; Rozwarski et al., 1996), groEL (1oel; Braig et al., 1995), hn-rnp (1ha1; Shamoo et al., 1997), penicillopepsin (3app; James & Sielecki, 1983), qaprtase (1qpo; Sharma et al., 1998), rh-dehalogenase (1bn7; Newman et al., 1999), rnase-s (1rge; Sevcik et al., 1996), rop (1f4n; Willis et al., 2000) and synaptotagmin (1dqv; Sutton et al., 1999). |
![[Figure 5]](ea5095fig5.jpg)
| BIOLOGICAL CRYSTALLOGRAPHY |
ISSN: 1399-0047
