3UFB
Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | 20 % (w/v) polyethylene glycol 8,000, 0.1 M at Hepes pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
2 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | 24 % (w/v) polyethyleneglycol 3350, 0.1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid at pH 7.5 and 10 mM -mercaptoethanol , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.899 | α = 90 |
b = 78.899 | β = 90 |
c = 165.802 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | CCD | ADSC QUANTUM 315r | 2008-11-12 | M | SINGLE WAVELENGTH | |||||||
2 | 2 | x-ray | CCD | ADSC QUANTUM 315r | 2011-09-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 4A | 1.0 | PAL/PLS | 4A |
2 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 0.98962 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 50 | 99.9 | 48972 | 2 | 2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution 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 | SAD | 1.8 | 5.999 | 0.1 | 47581 | 4811 | 99.46 | 0.1844 | 0.1809 | 0.2154 | 29.2993 |
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] | |
-2.9082 | -2.9082 | 5.8163 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.761 |
f_angle_d | 1.006 |
f_chiral_restr | 0.069 |
f_bond_d | 0.007 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3856 |
Nucleic Acid Atoms | |
Solvent Atoms | 542 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SOLVE | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |