4UBG
Resting state of rat cysteine dioxygenase C93G variant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4KWJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.3 | 291 | Hanging drops of 1.5 microL of approximately 7 mg/mL C93G-CDO (10mM sodiumphosphate, 20mM NaCl pH 7.5) and 0.6 microL wt-CDO seeds in their own growth solution (25% (w/v) polyethylene glycol 1500, 13mM succinate, 44mM sodiumphosphate, 44mM glycine) and 1.5 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (26% (w/v) polyethylene glycol 4000, 200 mM ammonium acetate, 100 mM sodium citrate). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 41.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.84 | α = 90 |
b = 57.84 | β = 90 |
c = 122.73 | 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 | 93 | CCD | ADSC QUANTUM 315r | 2013-03-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.953700 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 1.82 | 52.32 | 88.3 | 0.127 | 0.036 | 0.999 | 16.8 | 13.4 | 17317 | 16.83 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.82 | 1.86 | 100 | 1.246 | 0.359 | 0.819 | 1.9 | 12.9 | 1131 |
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 | FREE R-VALUE | 4kwj | 1.9 | 42.1004 | 14449 | 89.1 | 0.2019 | 0.2414 | 22.2998 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1517 |
Nucleic Acid Atoms | |
Solvent Atoms | 215 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
PHASER | phasing |