4CYF
The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | PROTEIN WAS AT 12 MG/ML IN 50 MM BIS-TRIS PH 6.5 WITH 50 MM NACL. THE RESERVOIR WAS 21% PEG 1500 WITH 10% (V/V) MALATE-MES-TRIS BUFFER AT PH 6.3. 200 NL PLUS 200 NL DROPS IN SITTING DROP PLATES. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.89 | 68.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 119.941 | α = 90 |
b = 119.941 | β = 90 |
c = 221.887 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | ADXV | 2013-11-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | Australian Synchrotron | MX2 |
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 | 2.25 | 48.3 | 99.8 | 0.14 | 15.2 | 14.8 | 77299 |
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 | 2.25 | 2.37 | 99.3 | 1.18 | 2.7 | 14.5 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SIRAS | THROUGHOUT | NONE | 2.25 | 105.51 | 73353 | 3872 | 99.72 | 0.19678 | 0.19548 | 0.22176 | RANDOM | 40.411 |
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] | |
0.88 | 0.88 | -1.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.705 |
r_dihedral_angle_4_deg | 19.277 |
r_dihedral_angle_3_deg | 13.557 |
r_dihedral_angle_1_deg | 6.679 |
r_mcangle_it | 4.082 |
r_scbond_it | 3.248 |
r_mcbond_it | 2.611 |
r_mcbond_other | 2.611 |
r_angle_refined_deg | 1.252 |
r_angle_other_deg | 0.832 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7264 |
Nucleic Acid Atoms | |
Solvent Atoms | 240 |
Heterogen Atoms | 112 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
Auto-Rickshaw | phasing |