2GJ3
Crystal structure of the FAD-containing PAS domain of the protein NifL from Azotobacter vinelandii.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 2.25M Ammonium sulfate, 5% ethanol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.111 | α = 90 |
b = 68.111 | β = 90 |
c = 302.064 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 | MAR CCD 165 mm | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 0.8266 | APS | 14-ID-B |
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 | 1.03 | 50 | 94.5 | 0.04 | 14.3 | 126308 |
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) | |||||||||||
1.03 | 1.07 | 50 | 63.1 | 0.462 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.04 | 40 | 126308 | 115137 | 11569 | 88.65 | 0.158 | 0.158 | 0.154 | 0.186 | RANDOM | 21.636 |
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] | |
-0.65 | -0.33 | -0.65 | 0.98 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.166 |
r_dihedral_angle_4_deg | 23.102 |
r_sphericity_free | 18.576 |
r_dihedral_angle_3_deg | 13.581 |
r_sphericity_bonded | 11.24 |
r_dihedral_angle_1_deg | 11.173 |
r_scangle_it | 6.926 |
r_mcangle_it | 5.926 |
r_scbond_it | 5.692 |
r_mcbond_it | 5.1 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1920 |
Nucleic Acid Atoms | |
Solvent Atoms | 340 |
Heterogen Atoms | 126 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SOLVE | phasing |