1YVG
Structural analysis of the catalytic domain of tetanus neurotoxin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1F82 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.2 | 293 | PEG 4000, magnesium chloride, hepes buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 106.61 | α = 90 |
b = 177.28 | β = 90 |
c = 54.55 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 2 |
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 | BRANDEIS - B4 | Mirrors | 2004-05-01 | M | MAD | |||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | Mirrors | 2004-09-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12C | 1.2810, 1.2824 | NSLS | X12C |
2 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.10 | NSLS | X25 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.4 | 50 | 99.4 | 0.12 | 7.5 | 9.4 | 20639 | 20639 | 47 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
2.4 | 2.49 | 99.1 | 7 | 9.3 | 2001 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MAD and Molecular replacement | THROUGHOUT | 1F82 | 2.6 | 50 | 15170 | 15170 | 1033 | 92.7 | 0.2182 | 0.2763 | Random | 46.6 |
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] | |
13.339 | 20.489 | -33.828 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 2.338 |
c_mcangle_it | 1.918 |
c_scbond_it | 1.488 |
c_angle_deg | 1.36447 |
c_mcbond_it | 1.114 |
c_bond_d | 0.008306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3222 |
Nucleic Acid Atoms | |
Solvent Atoms | 113 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
SCALEPACK | data scaling |
SOLVE | phasing |
CNS | refinement |
SHARP | phasing |