2NNC
Structure of the sulfur carrier protein SoxY from Chlorobium limicola f thiosulfatophilum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 294 | Ammonium phosphate, sodium acetate, DTT, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 42.8 |
2.41 | 47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.725 | α = 90 |
b = 120.114 | β = 90 |
c = 95.303 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | MARRESEARCH | 2005-02-02 | SINGLE WAVELENGTH | |||||||
2 | 1 | x-ray | 293 | CCD | MARRESEARCH | 2005-05-26 | SINGLE WAVELENGTH | |||||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 1.06 | EMBL/DESY, HAMBURG | BW7A |
2 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 1.04 | EMBL/DESY, HAMBURG | BW7A |
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 | 2.14 | 99 | 98.1 | 0.055 | 33.4 | 7.81 | 13122 | 5.6 |
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 | 2.14 | 2.2 | 97.8 | 0.393 | 5.6 | 831 |
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 (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MIR | THROUGHOUT | 2.14 | 20 | 12527 | 619 | 94.38 | 0.218 | 0.216 | 0.256 | RANDOM | 45.075 |
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] | |
-1.35 | 1.14 | 0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.415 |
r_dihedral_angle_4_deg | 19.826 |
r_dihedral_angle_3_deg | 13.338 |
r_dihedral_angle_1_deg | 6.364 |
r_scangle_it | 2.155 |
r_scbond_it | 1.354 |
r_angle_refined_deg | 1.317 |
r_mcangle_it | 0.788 |
r_angle_other_deg | 0.717 |
r_mcbond_it | 0.571 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1613 |
Nucleic Acid Atoms | |
Solvent Atoms | 47 |
Heterogen Atoms | 12 |
Software
Software | |
---|---|
Software Name | Purpose |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |