3H8L
The first X-ray structure of a sulfide:quinone oxidoreductase: insights into sulfide oxidation mechanism
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 293 | 2.2 M NH4H2PO4, 100 mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
2 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 293 | 2.2 M NH4H2PO4/K2HPO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 179.657 | α = 90 |
b = 179.657 | β = 90 |
c = 163.397 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2007-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.943 | ESRF | ID14-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.57 | 51.44 | 0.075 | 20 | 7.7 | 49511 | 2.6 | 67.89 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.57 | 2.71 | 96.8 | 0.51 | 2.6 | 4.3 | 6870 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SIRAS | THROUGHOUT | 2.57 | 29.68 | 49437 | 2509 | 99.17 | 0.1952 | 0.1938 | 0.2218 | RANDOM | 55.49 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.6536 | -0.6536 | 1.3072 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_dihedral_angle_d | 16.089 |
t_it | 0.898 |
t_angle_deg | 0.892 |
t_gen_planes | 0.012 |
t_bond_d | 0.006 |
t_trig_c_planes | 0.005 |
t_nbd |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5590 |
Nucleic Acid Atoms | |
Solvent Atoms | 267 |
Heterogen Atoms | 157 |
Software
Software | |
---|---|
Software Name | Purpose |
DNA | data collection |
SHARP | phasing |
BUSTER-TNT | refinement |
XDS | data reduction |
SCALA | data scaling |