3NK0
Complex of 6-hydroxy-L-nicotine oxidase with inhibitor bound at active site and turnover product at exit cavity
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3K7M | PDB code 3K7M |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 20mM Sodium phosphate; 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.87 | 68.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 163.677 | α = 90 |
b = 163.677 | β = 90 |
c = 163.677 | γ = 90 |
Symmetry | |
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Space Group | P 4 3 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 | MAR CCD 165 mm | mirror | 2003-03-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MPG/DESY, HAMBURG BEAMLINE BW6 | 1.05 | MPG/DESY, HAMBURG | BW6 |
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 | 2.15 | 20 | 99.4 | 0.1 | 14 | 4.5 | 41095 | 40984 | 2 | 33.98 |
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 | 2.15 | 2.19 | 99.6 | 0.718 | 2 | 4.5 | 2023 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 code 3K7M | 2.15 | 14.4 | 39048 | 38825 | 2054 | 99.43 | 0.16648 | 0.16422 | 0.21043 | RANDOM | 33.234 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.333 |
r_dihedral_angle_4_deg | 19.168 |
r_dihedral_angle_3_deg | 15.776 |
r_dihedral_angle_1_deg | 7.309 |
r_scangle_it | 5.785 |
r_scbond_it | 3.825 |
r_mcangle_it | 2.377 |
r_angle_refined_deg | 2.269 |
r_mcbond_it | 1.531 |
r_nbtor_refined | 0.326 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3272 |
Nucleic Acid Atoms | |
Solvent Atoms | 453 |
Heterogen Atoms | 123 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
MOLREP | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |