2ZO5
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with azide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OT4 | PDB ENTRY 2OT4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 278 | The drop contained 5ml of enzyme solution (14.5mg/ml) in 0.005M Tris-borat buffer (PH8.7) and 5ml reservoir solution. the reservoir solution contained 27% PEG400, 0.18M sodium citrate in 0.09M TRIS buffer (PH8.5), Complex with azide ion was obtained by soaking crystal in reservoir solution with 20mM sodium azide by 30 minute, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.04 | 75.58 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 193.027 | ¦Á = 90 |
b = 193.027 | ¦Â = 90 |
c = 193.027 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 3 |
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 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | EMBL/DESY, HAMBURG | X13 |
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 | 1.7 | 13 | 98.6 | 0.058 | 21 | 270000 |
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 | 1.7 | 1.71 | 98.3 | 0.489 |
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 | PDB ENTRY 2OT4 | 1.7 | 11.99 | 243353 | 12944 | 98.37 | 0.1521 | 0.15128 | 0.16763 | RANDOM | 16.487 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.318 |
r_dihedral_angle_4_deg | 17.321 |
r_dihedral_angle_3_deg | 12.258 |
r_dihedral_angle_1_deg | 6.013 |
r_scangle_it | 3.039 |
r_scbond_it | 1.971 |
r_angle_refined_deg | 1.519 |
r_mcangle_it | 1.287 |
r_angle_other_deg | 0.947 |
r_mcbond_it | 0.754 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8228 |
Nucleic Acid Atoms | |
Solvent Atoms | 1124 |
Heterogen Atoms | 817 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |