3WFE
Reduced and cyanide-bound cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with antibody fragment
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 | 100mM sodium citrate, pH 6.0, vapor diffusion, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.08 | 69.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.688 | α = 90 |
b = 107.381 | β = 90 |
c = 195.288 | 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 | 2012-01-24 | 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) | 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 | 2.49 | 50 | 99.1 | 0.076 | 0.076 | 24.231 | 7.4 | 66399 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.5 | 2.59 | 100 | 0.526 | 0.526 | 3.684 | 7.5 |
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 | 3O0R | 2.49 | 35.16 | 66111 | 3358 | 98.39 | 0.1907 | 0.1888 | 0.2274 | RANDOM | 61.6746 |
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] | |
-0.83 | -0.7 | 1.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.476 |
r_dihedral_angle_4_deg | 21.612 |
r_dihedral_angle_3_deg | 20.202 |
r_dihedral_angle_1_deg | 6.646 |
r_angle_refined_deg | 1.808 |
r_angle_other_deg | 0.98 |
r_chiral_restr | 0.112 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.012 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8060 |
Nucleic Acid Atoms | |
Solvent Atoms | 242 |
Heterogen Atoms | 201 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SPACE | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |