TABLE 3.
X-ray data collection, phasing, and structure refinement statistics
| Parameter | Value(s) for: |
|||
|---|---|---|---|---|
| GCYH-IB | GCYH-IB·Mn2+ | |||
| Structure refinement | ||||
| Resolution range (Å) | 45.9-2.2h | 30.33-2.04 | ||
| No. of reflections (working/free) | 42,833i/4,631 | 31,937/1,710 | ||
| No. of atoms | ||||
| Protein/water | 3,829/133 | 3,829/261 | ||
| Active-site metal ions | 2 | 2 | ||
| Other ions | 1 | 2 | ||
| Other ligands | 4 | 3 | ||
| Rcryst/Rfreej | 0.20/0.25 | 0.20/0.26 | ||
| rmsd bond length (Å) | 0.007 | 0.006 | ||
| rmsd bond angle (°) | 0.825 | 0.993 | ||
| Ramachandran plot—residues in: | ||||
| Favored regions (%) | 93.2 | 96.9 | ||
| Allowed regions (%) | 6.8 | 3.1 | ||
| Wilson B factor (Å2) | 40.3 | 37.4 | ||
| Data collection | ||||
| Space group | C2221 | C2221 | ||
| Data set | Sepeak | Seinflection | Seremote | |
| Unit cell (Å) | 91.7, 100.3, 114.1 | 91.7, 100.2, 114.0 | 91.8, 100.4, 114.1 | 92.2, 100.4, 113.9 |
| Wavelength (Å) | 0.9793 | 0.9795 | 0.9747 | 0.9761 |
| Resolution (Å) | 50.0-2.20 | 50.0-2.20 | 50.0-2.20 | 30.33-2.04 |
| Unique reflections | 26,718 (2,616)a | 26,761 (2,656) | 26,490 (2,136) | 33,675 (3,314) |
| Completeness (%) | 99.8 (99.0) | 99.8 (100.0) | 99.0 (92.0) | 99.8 (99.9) |
| Redundancy | 5.7 (5.0) | 5.8 (5.7) | 5.4 (3.5) | 4.5 (4.5) |
| Rmerge (%)b | 8.7 (61.5) | 7.5 (36.9) | 8.4 (89.1) | 7.1 (42.8) |
| I/σ(I) | 16.3 (2.4) | 17.6 (4.2) | 15.0 (3.5) | 11.0 (2.8) |
| Phasing statistics (29-2.30 Å) | ||||
| Rderc | 0.074d | 0.137 | ||
| Ranome | 0.069 | 0.059 | 0.058 | |
| RCullisf (isod/ano) | 0.49/0.73 | 0.83/0.72 | 0.84/0.86 | |
| Phasing powerg | ||||
| Centric | 0.06 | 0.11 | 0.16 | |
| Acentric | ||||
| isod | 0.06 | 0.09 | 0.15 | |
| ano | 1.20 | 1.46 | 1.10 | |
| FOM, overall | 0.34 | |||
| After DM | 0.83 | |||
| After Solomon | 0.85 | |||
| No. of Se sites | 15 | |||
Highest-resolution shell (2.2-2.28 Å for GCYH-IB, and 2.04-2.11 Å for GCYH-IB·Mn2+) information in parentheses.
Rmerge = 100 × (ΣhΣi|I(h) − I(h)i|)/ΣhΣiI(h)i, where I(h)i is the ith observation of reflection h and I(h) is the mean intensity of all observations of reflection h.
Rder = Σh|FPH − FP|/Σh|FP|, where |FP| and |FPH| are the observed structure factor amplitudes of the native and the derivative, respectively.
The dispersive differences were treated as isomorphous replacement information where the data collected at a wavelength of 0.9747 Å are treated as native data.
Ranom = Σh|FPH+ − FPH−|/Σh|FPH|, where |FPH+| and |FPH−| are the Friedel pair observed structure factor amplitudes of the derivative at a given wavelength, and FPH is their average.
RCullis = Σh[|FH| − (|FPH| − |FP|)]/Σh(|FPH| − |FP|), where |FH| is the calculated heavy-atom structure factor for reflection h.
PPdisp= (1/Nrefl)Σh[||FPH| − |FP||/∫02π(|FPH − FPHcalc|) P(ϕ) d(ϕ)], where P(ϕ) is the probability of a phase value of ϕ for reflection h. PPano = (1/Nrefl)Σh[|ΔobsANO|/∫02π(|ΔobsANO − ΔcalcANO|) P(ϕ) d(ϕ)], where ΔobsANO and ΔcalcANO are the Friedel pair differences in the observed and calculated structure factor amplitudes, respectively, for reflection h.
During density modification, structure factors were calculated for remote-wavelength data in the resolution range 2.3 to 2.2 Å.
Anomalous pairs treated as separate reflections.
Crystallographic R factor = 100 × (Σh||Fobs(h)| − |Fcalc(h)||)/Σh|Fobs(h)|, where Fobs(h) and Fcalc(h) are the observed structure factor amplitude and the structure factor amplitude calculated from the model, respectively. The free R factor was monitored with 10% and 5% of the data excluded from refinement for GCYH-IB and GCYH-IB·Mn2+, respectively.