3N9B
Crystal Structure of the P. aeruginosa LigD phosphoesterase domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | Crystallization was carried out in sitting-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 1.3 mM PaePEC2 and 2mM MnCl2 and reservoir solution containing PEG 5000 monomethylether (MME) (20 - 30%), 100 mM 2-(N-morpholino) ethanesulfonic acid (MES) pH 6.8 - 7.0, 200 mM ammonium sulfate, and 10 mM yttrium (III) chloride at 22 C. , VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.583 | α = 102.32 |
b = 45.55 | β = 109.43 |
c = 53.384 | γ = 104.59 |
Symmetry | |
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Space Group | P 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 | 130 | CCD | ADSC QUANTUM 315 | See NSLS X25 Beamline Description | 2010-02-20 | M | SINGLE WAVELENGTH | |||||
2 | 1 | CCD | ADSC QUANTUM 210 | See NSLS X12C Beamline Description | 2010-02-20 | |||||||||
3 | 1 | IMAGE PLATE | RIGAKU RAXIS IV++ | Osmic confocal mirrors | 2010-02-10 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12C | 1.19 0.99 0.73 | NSLS | X12C |
2 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.19 0.99 0.73 | NSLS | X25 |
3 | ROTATING ANODE | RIGAKU RU300 | 1.54 |
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 | 1.92 | 50 | 95.6 | 0.087 | 25.9 | 7.4 | 25728 | 24596 | -3 | 26 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.92 | 1.95 | 93 | 4.8 | 2.1 | 1272 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MIR | 1.92 | 37.395 | 0.06 | 23992 | 2387 | 92.95 | 0.1527 | 0.1475 | 0.1988 | 10% selected at random in CCP4/Unique |
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] | |
5.3212 | -1.2709 | -1.1842 | -1.6351 | 0.4754 | -3.7302 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.969 |
f_angle_d | 1.249 |
f_chiral_restr | 0.1 |
f_bond_d | 0.01 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2439 |
Nucleic Acid Atoms | |
Solvent Atoms | 358 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SOLVE | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |