2C3P
CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KEK | PDB ENTRY 1KEK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6 | 10% PEG6000, 100MM MGCL2, 100MM NA CACODYLATE PH 6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 48.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.966 | α = 90 |
b = 145.84 | β = 90 |
c = 210.822 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 287 | CCD | ADSC CCD | 2002-12-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 2.33 | 50 | 97.5 | 0.01 | 11.73 | 4.7 | 524442 | 2 | 16.5 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.33 | 2.49 | 95.6 | 0.03 | 5.37 | 4.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1KEK | 2.33 | 47.37 | 111926 | 5637 | 98.3 | 0.171 | 0.171 | 0.223 | RANDOM | 25.4 |
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] | |
-3.91 | 1.59 | 2.33 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.2 |
c_scangle_it | 5.31 |
c_scbond_it | 4.03 |
c_mcangle_it | 3.38 |
c_mcbond_it | 2.4 |
c_angle_deg | 1.6 |
c_improper_angle_d | 0.96 |
c_bond_d | 0.012 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 18766 |
Nucleic Acid Atoms | |
Solvent Atoms | 851 |
Heterogen Atoms | 116 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
XDS | data reduction |
XSCALE | data scaling |
CNS | phasing |