3HYV
3-D X-Ray structure of the sulfide:quinone oxidoreductase from the hyperthermophilic bacterium Aquifex aeolicus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291 | 4% PEG 400 (V/V), 0.1M NA-MES (SODIUM 2-(N-MORPHOLINO)-ETHANESULFONATE), 2M AMMONIUM SULFATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.73 | 54.92 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 112.85 | α = 90 |
b = 154.92 | β = 90 |
c = 178.04 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 | MARMOSAIC 225 mm CCD | dynamically bendable mirror | 2008-02-24 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | PIXEL | PSI PILATUS 6M | dynamically bendable mirror | 2008-02-24 | M | MAD | |||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.91984 | SLS | X10SA |
2 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.14000, 1.14050, 1.13010, 1.03864 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.3 | 50 | 97.9 | 14.87 | 3.47 | 135807 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1,2 | 2.3 | 2.4 | 87.9 | 3.44 | 2.47 |
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 | MIRAS | THROUGHOUT | 2.3 | 20.04 | 128783 | 6821 | 97.94 | 0.19534 | 0.19321 | 0.23537 | RANDOM | 38.517 |
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] | |
1.32 | -0.09 | -1.23 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.217 |
r_dihedral_angle_4_deg | 20.052 |
r_dihedral_angle_3_deg | 15.77 |
r_dihedral_angle_1_deg | 5.351 |
r_scangle_it | 1.654 |
r_angle_refined_deg | 1.254 |
r_scbond_it | 1.043 |
r_mcangle_it | 0.648 |
r_mcbond_it | 0.412 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 20016 |
Nucleic Acid Atoms | |
Solvent Atoms | 571 |
Heterogen Atoms | 768 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data scaling |
SHARP | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |