5LLD
Flavodiiron core of Escherichia coli flavorubredoxin in the reduced form.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 304 | 1.0UL OF PROTEIN AT15 MG/ML WITH 0.8UL OF CRYSTALLIZATION SOLUTION (0.2M NA-CACODYLATE PH 6.5, 0.2 M MGACETATE, 20% PEG8000) and 0.2UL OF 0.1M HEXAMINE COBALT (III). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.95 | 58.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 151.7 | α = 90 |
b = 151.7 | β = 90 |
c = 96.5 | γ = 120 |
Symmetry | |
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Space Group | P 6 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 | 2008-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.8726 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.65 | 45.34 | 91 | 0.157 | 5.9 | 6.3 | 17773 | 18 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.65 | 2.74 | 90.3 | 0.8 | 1.5 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FOURIER SYNTHESIS | FREE R-VALUE | 4d02 | 2.651 | 45.292 | 0.35 | 1713 | 17132 | 87.72 | 0.1899 | 0.185 | 0.246 | random |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-9.168 | -9.168 | -2.4335 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 10.846 |
f_angle_d | 0.566 |
f_chiral_restr | 0.044 |
f_bond_d | 0.015 |
f_plane_restr | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3200 |
Nucleic Acid Atoms | |
Solvent Atoms | 128 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHENIX | phasing |