4L0Q
Crystal structure of S-nitrosoglutathione reductase from Arabidopsis thaliana, C370A/C373A double mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3UKO | PDB ENTRY 3UKO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 2.1 M ammonium sulfate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.731 | α = 90 |
b = 92.731 | β = 90 |
c = 173.558 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | MARMOSAIC 325 mm CCD | 2006-05-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.9795 | SSRL | BL9-2 |
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 | 1.95 | 28.65 | 99.8 | 0.091 | 15.6 | 12.1 | 63603 | 63603 | 46.1 |
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 | 1.95 | 2.02 | 100 | 0.44 | 4.4 | 12.2 | 6274 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 3UKO | 1.95 | 28.65 | 59791 | 59791 | 3192 | 98.86 | 0.20219 | 0.20219 | 0.19964 | 0.25109 | RANDOM | 42.184 |
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] | |
-0.02 | -0.02 | -0.02 | 0.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.503 |
r_dihedral_angle_4_deg | 21.592 |
r_dihedral_angle_3_deg | 15.232 |
r_dihedral_angle_1_deg | 7.063 |
r_angle_refined_deg | 2.037 |
r_angle_other_deg | 0.923 |
r_chiral_restr | 0.116 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5686 |
Nucleic Acid Atoms | |
Solvent Atoms | 385 |
Heterogen Atoms | 122 |
Software
Software | |
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Software Name | Purpose |
XDISPLAYF | data collection |
REFMAC | refinement |
d*TREK | data reduction |
CrystalClear | data scaling |
REFMAC | phasing |