6U7N
Crystal structure of neurotrimin (NTM)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5UV6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 293.15 | Protein: 5.4 mg/ml NTM in 10 mM HEPES, pH 8.0, 150 mM sodium chloride Reservoir Solution: 2.5 M NaCl, 100 mM sodium acetate pH 4.5, 200 mM lithium sulfate Crystallization Drop: 2 micro-Liters NTM + 2 micro-Liters Reservoir Solution Single crystals grew to a size of ~250 x 150 micro-meters within 7-10 days. Crystals harvested from the crystallization drops were cryo-protected in reservoir solution containing 20% (v/v) ethylene glycol and then flash cooled by plunging into liquid nitrogen |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 106.049 | α = 90 |
b = 106.049 | β = 90 |
c = 227.819 | γ = 90 |
Symmetry | |
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Space Group | I 41 |
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 | ADSC QUANTUM 315 | 2018-05-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 0.999990 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 3.32 | 46.431 | 99.4 | 0.062 | 0.07 | 0.032 | 13 | 4.6 | 18288 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 3.32 | 3.38 | 93.4 | 1.328 | 1.545 | 0.776 | 0.467 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5UV6 | 3.321 | 46.43 | 1.36 | 15249 | 504 | 82.39 | 0.2298 | 0.2291 | 0.2501 | 79.78 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2017 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 165 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
PHENIX | phasing |