4TVW
Resorufin ligase with bound resorufin-AMP analog
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 2 uL of 5.6 mg/mL resorufin ligase containing 1 mM resorufin sulfamoyladenosine, 1 mM Mg(OAc)2, and 1 mM dithiothreitol mixed with 2 uL of precipitant solution (11% PEG 20,000, 0.15 M MES:NaOH, pH 6.5). Dark, and red colored crystalline plates appeared after ~ 5 days. Crystals were looped and washed through a cryoprotection solution of 80% precipitant solution (12% PEG 20,000, 0.2 M MES:NaOH, pH 6.5) and 20% glycerol. Crystals were then cryocooled by direction submersion into liquid nitrogen. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.28 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.354 | α = 90 |
b = 99.932 | β = 105.79 |
c = 107.284 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | PIXEL | DECTRIS PILATUS 6M | 2012-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.9795 | APS | 24-ID-C |
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 | 3.5 | 49.98 | 92 | 0.139 | 7.8 | 2.8 | 21542 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
3.5 | 3.63 | 66.7 | 0.265 | 2.333 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | NONE | 3.505 | 49.966 | 1.31 | 20497 | 1049 | 87.14 | 0.2032 | 0.2007 | 0.2484 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.207 |
f_angle_d | 0.838 |
f_chiral_restr | 0.054 |
f_bond_d | 0.003 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10588 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 180 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |