4CYG
The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4CYF | PDB ENTRY 4CYF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 281 | CRYSTALLIZATION CONDITIONS: PROTEIN AT 12 MG/ML IN 50 MM BIS-TRIS PH 6.5 WITH 50 MM NACL. RESERVOIR CONDITIONS WERE 21% PEG 1500 WITH 10% (V/V) MALATE-MES-TRIS BUFFER AT PH 6.3. DROPS WERE 200 NL PLUS 200 NL IN SITTING DROP PLATES AT 8C. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.88 | 68.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 120.093 | α = 90 |
b = 120.093 | β = 90 |
c = 221.9 | 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 | ADSC CCD | 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 | 2.3 | 48.3 | 99.6 | 0.15 | 15.6 | 14.9 | 72390 |
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 | 2.3 | 2.42 | 99.3 | 1.24 | 2.6 | 15.2 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4CYF | 2.3 | 105.62 | 68703 | 3638 | 99.42 | 0.18765 | 0.18624 | 0.21444 | RANDOM | 36.863 |
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] | |
0.24 | 0.24 | -0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.508 |
r_dihedral_angle_4_deg | 17.562 |
r_dihedral_angle_3_deg | 12.708 |
r_dihedral_angle_1_deg | 6.551 |
r_mcangle_it | 3.134 |
r_scbond_it | 2.577 |
r_mcbond_it | 1.962 |
r_mcbond_other | 1.959 |
r_angle_refined_deg | 1.24 |
r_angle_other_deg | 0.82 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7267 |
Nucleic Acid Atoms | |
Solvent Atoms | 307 |
Heterogen Atoms | 168 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |