Table 1.
Data Collection and Refinement Statistics, Glycine-Bound VCII RNA
| Crystal | Soaked in 2 mM [Ir(NH3)6]Cl3 | Native Co-crystals |
Native Soaking |
|||
|---|---|---|---|---|---|---|
|
| ||||||
| PDB ID | 3OWZ | 3OWI | 3OWW | |||
| Data Collection | ||||||
|
| ||||||
| Space group | P3221 | P3221 | P3221 | |||
| Cell dimensions a,b,c (Å) | 82.7, 82.7, 149.5 | 83.8, 83.8, 198.7 | 83.5, 83.5, 198.5 | |||
| Peak | Inflection | Remote (L) | Remote (H) | |||
| Wavelength (Å) | 1.1053 | 1.1056 | 1.1256 | 1.0859 | 1.0809 | 1.0750 |
| Resolutiona | 20.00-2.95 (3.00-2.95) |
20.00-2.95 (3.00-2.95) |
20.00-3.00 (3.05-3.00) |
20.00-3.05 (3.10-3.05) |
20.00-2.85 (2.95-2.85) |
20.00-2.80 (2.90-2.80) |
| Rmerge (%)a | 9.0 (38.5) | 7.5 (47.7) | 7.0 (52.5) | 8.4 (42.3) | 5.9 (57.2) | 5.5 (45.1) |
| <I>/σ(I)a | 38.0 (6.1) | 35.0 (4.6) | 33.0 (4.6) | 33.0 (6.0) | 58.2 (5.5) | 41.2 (4.1) |
| Completeness (%)a | 99.9 (100.0) | 99.9 (100.0) | 99.9 (99.8) | 99.9 (99.8) | 98.6 (98.5) | 99.3 (99.4) |
| Unique reflectionsa | 12,921 (620) | 12,945 (632) | 12,318 (608) | 11,724 (548) | 19,420 (1,893) | 20,267 (1,983) |
| Redundancy | 6.9 (7.1) | 6.9 (7.0) | 6.9 (7.0) | 6.9 (7.1) | 14.9 (15.4) | 6.0 (6.1) |
|
| ||||||
| Phasing | ||||||
|
| ||||||
| Number of [Ir(NH3)6] 3+sites | 23 | |||||
| Figure of merit (acentric/centric) | 0.56/0.36 | |||||
|
| ||||||
| Structure Refinement | ||||||
|
| ||||||
| Resolution (Å) | 20.0-2.95 | 20.00-2.85 | 20.00-2.80 | |||
| Working set reflections | 11,610 | 18,400 | 18,182 | |||
| Test set reflections | 1,280 | 996 | 2,065 | |||
| Rfactor / Rfree (%) | 21.0 / 23.1 | 20.8 / 23.6 | 20.4 / 23.6 | |||
|
| ||||||
| Number of Nonhydrogen Atoms | ||||||
|
| ||||||
| RNA | 3,703 | 3,807 | 3,785 | |||
| Glycine | 10 | 10 | 10 | |||
| Cations | 171 | 33 | 33 | |||
|
| ||||||
| Average B-factors (Å2) | ||||||
|
| ||||||
| RNA | 58.5 | 36.8 | 33.6 | |||
| Glycine | 44.5 | 34.1 | 28.5 | |||
| Cations | 37.4 | 74.6 | 54.2 | |||
|
| ||||||
| RMSD values | ||||||
|
| ||||||
| Bond lengths (Å) | 0.005 | 0.005 | 0.005 | |||
| Bond angles (°) | 0.976 | 1.024 | 1.003 | |||
| Estimated coordinate errorb | 0.272 | 0.253 | 0.248 | |||
a
Values for the highest resolution shell are in parentheses.
b
Estimated coordinate error based on maximum likelihood was calculated with REFMAC (Murshudov et al., 1997).