5GUX
Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3O0R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6 | 277 | 24% PEG 400, 0.1M SODIUM CITRATE, 50mM SODIUM CHLORIDE, 20mM MAGNESIUM CHLORIDE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.99 | 69.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.843 | α = 90 |
b = 105.379 | β = 90 |
c = 192.577 | 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 | 100 | CCD | RAYONIX MX225HE | mirrors | 2013-06-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.00 | 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 | 3.3 | 40 | 98.3 | 0.131 | 7.3 | 4.5 | 27449 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.3 | 3.36 | 100 | 0.456 | 0.808 | 4.3 |
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 | 3O0R | 3.3 | 39.39 | 26029 | 1369 | 96.91 | 0.2121 | 0.2092 | 0.2675 | RANDOM | 88.715 |
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] | |
-3.88 | 0.95 | 2.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.733 |
r_dihedral_angle_3_deg | 18.68 |
r_dihedral_angle_4_deg | 16.279 |
r_dihedral_angle_1_deg | 6.388 |
r_angle_refined_deg | 1.627 |
r_chiral_restr | 0.103 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8060 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 205 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Coot | model building |
HKL-2000 | data reduction |
PHASES | phasing |