3KLJ
Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 35% (v/v) PEG 400, 0.1M Tris-HCl pH 8.5, 0.15M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 98.576 | α = 90 |
b = 98.576 | β = 90 |
c = 88.267 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | 90 | CCD | ADSC QUANTUM 315 | 2008-11-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0000 | SPring-8 | BL41XU |
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 | 2.1 | 20 | 99.9 | 0.052 | 11.7 | 4.2 | 25983 | 25983 | 38.3 |
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 | 2.1 | 2.21 | 100 | 0.442 | 3.2 | 4.2 | 4806 |
Refinement
Statistics | |||||||||||||||||||
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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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.1 | 20 | 24627 | 1319 | 99.85 | 0.2157 | 0.21366 | 0.25435 | RANDOM | 19.958 |
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] | |
-0.1 | -0.1 | 0.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.303 |
r_dihedral_angle_4_deg | 18.859 |
r_dihedral_angle_3_deg | 17.859 |
r_dihedral_angle_1_deg | 6.453 |
r_scangle_it | 2.114 |
r_scbond_it | 1.323 |
r_angle_refined_deg | 1.196 |
r_mcangle_it | 0.853 |
r_mcbond_it | 0.46 |
r_chiral_restr | 0.086 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2890 |
Nucleic Acid Atoms | |
Solvent Atoms | 168 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
BSS | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |