7XCM
Crystal structure of sulfite MttB structure at 3.2 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7XCL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 283 | 1 ul protein (8 mg/mL MttB in 20 mM potassium phosphate buffer pH 7.4, 500 mM NaCl, 240 mM imidazole, 20% glycerol), 1 ul reservoir (4% MPD, 0.1 M citric acid pH 4.5) solutions, reservoir solution containing saturated sodium dithionite |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.11 | 70.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 174.84 | α = 90 |
b = 174.84 | β = 90 |
c = 300.121 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | IMAGE PLATE | RIGAKU RAXIS IV | 2018-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ | 1.54187 |
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 | 3.2 | 20 | 85.4 | 0.196 | 2.6 | 2.7 | 74099 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.2 | 3.27 | 0.254 |
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-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 7xcl | 3.2 | 20 | 74084 | 7479 | 84.5 | 0.1665 | 0.243 | 53.0752 |
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] | |
-10.096 | -10.096 | 20.192 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 14.207 |
c_scbond_it | 11.443 |
c_mcangle_it | 10.164 |
c_mcbond_it | 7.024 |
c_angle_d | 1.277 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 22588 |
Nucleic Acid Atoms | |
Solvent Atoms | 165 |
Heterogen Atoms | 144 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |
PHASER | phasing |