1VR3
Crystal structure of Acireductone dioxygenase (13543033) from Mus musculus at 2.06 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 5.6 | 277 | 5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.71 | 66.57 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 79.136 | ¦Á = 90 |
b = 79.136 | ¦Â = 90 |
c = 114.128 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 41 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 | fixed-height exit beam, toroidal focusing mirror | 2004-11-10 | M | MAD | |||||
2 | 1 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 0.979735,0.979562,0.956885 | ALS | 5.0.2 |
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 | 2.06 | 28.54 | 100 | 0.101 | 13.6 | 6.8 | 23148 | 43.37 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.06 | 2.17 | 100 | 0.864 | 2.2 | 5.4 | 3314 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.06 | 28.53 | 21908 | 1183 | 99.94 | 0.16387 | 0.16229 | 0.19532 | RANDOM | 37.722 |
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] | |
-0.48 | -0.48 | 0.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.216 |
r_dihedral_angle_3_deg | 13.935 |
r_dihedral_angle_4_deg | 11.433 |
r_scangle_it | 8.382 |
r_dihedral_angle_1_deg | 6.425 |
r_scbond_it | 6.033 |
r_mcangle_it | 3.504 |
r_mcbond_it | 2.887 |
r_angle_refined_deg | 1.436 |
r_angle_other_deg | 0.799 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1484 |
Nucleic Acid Atoms | |
Solvent Atoms | 169 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
SCALA | data scaling |
autoSHARP | phasing |
REFMAC | refinement |
XDS | data reduction |
CCP4 | data scaling |