4JR9
Crystal structure of nitrate/nitrite exchanger NarK
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3TT1 | PDB entries 3TT1, 1F8T, 3TT3, 1MRC |
experimental model | PDB | 1F8T | PDB entries 3TT1, 1F8T, 3TT3, 1MRC |
experimental model | PDB | 3TT3 | PDB entries 3TT1, 1F8T, 3TT3, 1MRC |
experimental model | PDB | 1MRC | PDB entries 3TT1, 1F8T, 3TT3, 1MRC |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 3.5 | 277 | 28% PEG400, 0.1 M citric acid pH 3.5, 0.1M NaCl, 0.1M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.06 | 69.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 138.266 | α = 90 |
b = 86.545 | β = 115.41 |
c = 144.789 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2012-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.999973 | ALS | 8.2.2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.6 | 50 | 99.5 | 0.097 | 19.8 | 7.1 | 47606 | 1.5 | 65 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.6 | 2.64 | 93.2 | 0.892 | 1.5 | 4.6 | 2237 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 entries 3TT1, 1F8T, 3TT3, 1MRC | 2.6 | 50 | 47471 | 45063 | 2408 | 99.45 | 0.23054 | 0.22889 | 0.26132 | RANDOM | 66.779 |
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] | |
-2.45 | -0.56 | -1.3 | 3.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.604 |
r_dihedral_angle_3_deg | 19.707 |
r_dihedral_angle_4_deg | 18.506 |
r_dihedral_angle_1_deg | 5.707 |
r_angle_refined_deg | 1.312 |
r_chiral_restr | 0.086 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6273 |
Nucleic Acid Atoms | |
Solvent Atoms | 45 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
BOS | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |