3JVN
Crystal Structure of the acetyltransferase VF_1542 from Vibrio fischeri, Northeast Structural Genomics Consortium Target VfR136
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | microbatch, under oil | 5.5 | 277 | Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 0.1M Bis Tris (pH 5.5), 1% PEG 3350, and 0.1M ammonium sulfate, microbatch, under oil, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.714 | α = 90 |
b = 105.332 | β = 90 |
c = 73.872 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | MAR CCD 165 mm | mirrors | 2009-09-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.9791 | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.6 | 30 | 76.8 | 0.048 | 0.054 | 24.93 | 3.6 | 10548 | 8101 | 2 | 2 | 31.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.6 | 2.69 | 52.3 | 0.082 | 0.101 | 7.97 | 2.3 | 1051 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.61 | 19.13 | 2 | 2 | 10531 | 8088 | 417 | 76.8 | 0.335 | 0.334 | 0.233 | 0.273 | RANDOM | 40.1 |
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] | |
-5.63 | 14.5 | -8.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.2 |
c_angle_deg | 1.1 |
c_improper_angle_d | 0.7 |
c_bond_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1002 |
Nucleic Acid Atoms | |
Solvent Atoms | 27 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
SnB | phasing |
REFMAC | refinement |