3BGU
Crystal structure of a dimeric ferredoxin-like protein of unknown function (tfu_0763) from thermobifida fusca yx at 1.50 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 277 | NANODROP, 50.0% Ethylene glycol, 5.0% PEG 1000, 0.1M Sodium acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.63 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 44.07 | ¦Á = 90 |
b = 35.27 | ¦Â = 104.09 |
c = 76.63 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 2 1 |
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 | ADSC QUANTUM 315 | 2007-10-04 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.9537, 0.9798, 0.9797 | ALS | 8.2.2 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.5 | 27.206 | 91.4 | 0.044 | 11.24 | 35092 | -3 | 21.273 |
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 | 1.5 | 1.55 | 61.1 | 0.397 | 1.6 |
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 | MAD | THROUGHOUT | 1.5 | 27.206 | 35091 | 1762 | 94.9 | 0.199 | 0.197 | 0.237 | RANDOM | 7.727 |
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] | |
0.48 | -0.6 | -0.2 | -0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.905 |
r_dihedral_angle_4_deg | 14.898 |
r_dihedral_angle_3_deg | 13.398 |
r_dihedral_angle_1_deg | 11.611 |
r_scangle_it | 5.568 |
r_scbond_it | 4.488 |
r_mcangle_it | 2.59 |
r_mcbond_it | 1.798 |
r_angle_refined_deg | 1.771 |
r_angle_other_deg | 0.973 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1610 |
Nucleic Acid Atoms | |
Solvent Atoms | 176 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
ADSC | data collection |
XDS | data reduction |
SHELXD | phasing |
SHARP | phasing |