Table 2. I-SAD structure solution and refinement statistics.
Protein | ||||||||
NarQ | KR2 | MACR | A2AAR-BRIL-ΔC | |||||
Structure solution and initial model building | ||||||||
Data | Eight anomalous + native |
Data set #8 + native |
Four anomalous + native |
Three anomalous + native |
Seven anomalous + native |
|||
Method | I-SAD | I-SIRAS | I-SAD | I-SIRAS | I-SAD | I-SIRAS | I-SAD | I-SIRAS |
Initial resolution range (Å) | 60−2.7 | 60−2.7 | 60−2.5 | 60−2.5 | 60−2.0 | 60−2.0 | 60−2.8 | 60−2.8 |
Number of residues in the protein |
237 | 288 | 220 | 447 | ||||
Substructure | 14·I | 10·I | 16·I | 17·I | 26·I† 14·I |
16·I | 8·I | 10·I |
Resolution cutoff for substructure search (Å) |
3.0 | 2.8 | 2.8 | 2.8 | 2.5 | 2.9 | 3.7 | 3.9 |
Resolution extension by native data (Å) |
1.95 | 1.95 | 2.5 | 2.5 | 2.0 | 2.0 | 2.4 | 2.4 |
CCall/CCweak | 40/15.4 | 31.8/18.1 | 42.6/20.7 | 37.7/25.1 | 28.8/15.3 | 29.8/19.6 | 35.0/14.8 | 36.7/21.4 |
Solvent content used in SHELXE (%) |
47 | 47 | 58 | 59 | 50 | 50 | 49 | 49 |
CCmap, highest-resolution shell (%) | 74 | 77 | 67 | 84 | 87 | 81 | 73 | 74 |
Number of Ala residues traced by SHELXE |
178 | 187 | 212 | 208 | 190 | 272 | 155 | 250 |
Rwork/Rfree after initial model building (%) |
23.0/28.5* | 24.8/32.9* | 22.4/30.1* | 22.6/29.3* | 24.2/29.2†‡ 29.4/32.7‡ | 29.7/46.2* 29.9/32.7‡ | 30.7/32.9‡ | 29.5/45.8* |
Number of residues built in initial model building |
215* | 216* | 235* | 265* | 343†‡ 300‡ | 69* 319‡ | 277‡ | 168* |
Structure refinement | ||||||||
Data set (see Table 1) | 8 | 3 | 3 | 2 | ||||
Rwork/Rfree final (%) | 19.0/26.2 | 19.0/22.6 | 17.7/21.9 | 23.4/29.4 | ||||
Number in the ASU (asymmetric unit) | ||||||||
Protein residues | 223 | 268 | 431 | 388 | ||||
Water molecules | 60 | 49 | 78 | 64 | ||||
Iodide ions | 12 | 20 | 22 | 6 | ||||
Averaged B-factors (Å2) | ||||||||
Protein residues | 43 | 40 | 38 | 38 | ||||
Water molecules | 34 | 44 | 47 | 27 | ||||
Iodide ions | 70 | 66 | 71 | 50 | ||||
Ramachandran plot | ||||||||
Preferred | 216 (99.1%) | 259 (97.4%) | 419 (98.4%) | 373 (97.9%) | ||||
Allowed | 2 (0.9%) | 6 (2.2%) | 7 (1.6%) | 7 (1.8%) | ||||
Outliers | 0 | 1 (0.4%) | 0 | 1 (0.3%) |
*Initial model built by ARP-wARP.
†Phasing carried out using phenix.autosol (all others used SHELXC/D/E).
‡Initial model built by phenix.autobuild.