4F6T
The crystal structure of the molybdenum storage protein (MoSto) from Azotobacter vinelandii loaded with various polyoxometalates
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OGX | PDB entry 2OGX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 277 | NH4H2PO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
2 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 283 | NH4H2PO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 115.74 | α = 90 |
b = 115.74 | β = 90 |
c = 233.62 | γ = 120 |
Symmetry | |
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Space Group | P 63 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 2009-03-03 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2010-06-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.008 | SLS | X10SA |
2 | SYNCHROTRON | ESRF BEAMLINE ID29 | 1.71 | ESRF | ID29 |
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 | 1.6 | 46 | 90 | 0.085 | 13.45 | 4.4 | 121767 | 109553 | -3 | 22.705 |
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) | |||||||||||
1,2 | 1.6 | 1.7 | 59.4 | 0.548 | 3.61 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2OGX | 1.6 | 46 | -3 | 121767 | 109551 | 5467 | 89.99 | 0.1421 | 0.1421 | 0.1394 | 0.1733 | RANDOM | 22.3128 |
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] | |
-0.09 | -0.05 | -0.09 | 0.14 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.965 |
r_dihedral_angle_4_deg | 16.84 |
r_dihedral_angle_3_deg | 13.894 |
r_scangle_it | 8.005 |
r_dihedral_angle_1_deg | 6.185 |
r_angle_refined_deg | 5.8 |
r_scbond_it | 5.727 |
r_mcangle_it | 3.927 |
r_rigid_bond_restr | 3.047 |
r_mcbond_it | 2.668 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3800 |
Nucleic Acid Atoms | |
Solvent Atoms | 524 |
Heterogen Atoms | 172 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
EDNA | data collection |
XDS | data reduction |
REFMAC | phasing |