3R5B
Pseudomonas aeruginosa DapD (PA3666) in complex with L-2-aminopimelate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 293 | 19-20% of PEG3350, 0.3-0.4M succinate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.038 | α = 90 |
b = 102.002 | β = 89.97 |
c = 134.903 | 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 | CCD | MARMOSAIC 225 mm CCD | 2009-10-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-3 | 1.00 | MAX II | I911-3 |
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 | 2.5 | 37 | 95.9 | 0.144 | 0.144 | 6.7 | 3.4 | 72498 | 72498 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | FOURIER SYNTHESIS | THROUGHOUT | 2.51 | 36.88 | 68844 | 68844 | 3632 | 93.94 | 0.25149 | 0.25019 | 0.27567 | RANDOM | 21.868 |
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] | |
-1.7 | 0.7 | 0.72 | 0.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.965 |
r_dihedral_angle_4_deg | 18.114 |
r_dihedral_angle_3_deg | 16.075 |
r_dihedral_angle_1_deg | 6.068 |
r_angle_refined_deg | 1.242 |
r_scangle_it | 1.103 |
r_angle_other_deg | 0.968 |
r_scbond_it | 0.648 |
r_mcangle_it | 0.455 |
r_mcbond_it | 0.254 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14081 |
Nucleic Acid Atoms | |
Solvent Atoms | 256 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |