4BF9
Crystal structure of E. coli dihydrouridine synthase C (DusC) (selenomethionine derivative)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6.5 | MOLECULAR DIMENSIONS MORPHEUS SCREEN CONDITION D3, pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.8 | 68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.14 | α = 90 |
b = 94.14 | β = 90 |
c = 119.68 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC CCD | 2010-05-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.6 | 59.8 | 99.9 | 0.12 | 12.2 | 7.7 | 17124 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.6 | 2.74 | 100 | 0.843 | 2.2 | 7.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | SAD | THROUGHOUT | NONE | 2.6 | 58.17 | 16226 | 860 | 99.64 | 0.17858 | 0.17668 | 0.21447 | RANDOM | 53.164 |
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] | |
0.91 | 0.91 | -1.82 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.194 |
r_dihedral_angle_4_deg | 19.832 |
r_dihedral_angle_3_deg | 14.521 |
r_dihedral_angle_1_deg | 6.274 |
r_scangle_it | 3.067 |
r_mcangle_it | 2.308 |
r_scbond_it | 1.883 |
r_mcbond_it | 1.456 |
r_mcbond_other | 1.456 |
r_angle_refined_deg | 1.431 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2495 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 31 |
Software
Software | |
---|---|
Software Name | Purpose |
BUCCANEER | model building |
SCALA | data scaling |
SHELXCD | phasing |
PHASER | phasing |
PARROT | phasing |
BUCCANEER | phasing |
REFMAC | refinement |