4OZE
A.aolicus LpxC in complex with native product
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GO4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293 | Protein buffer: 25 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 0.1 mM ZnSO4, 5% glycerol Well solution: 15% PEG 550 MME, 15% PEG 20K, 100 mM Morpheus buffer 1, 10% Morpheus alchohols. drop formed by 1:1 mix |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.84 | 56.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.332 | α = 90 |
b = 101.332 | β = 90 |
c = 123.553 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | 140 | PIXEL | DECTRIS PILATUS 6M | 2013-07-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.61 | 87.76 | 100 | 0.073 | 21.2 | 12.4 | 92692 | 24.31 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.61 | 1.8 | 100 | 0.738 | 0.219 | 3.3 | 12.3 | 26277 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2GO4 | 1.61 | 87.76 | 92630 | 4637 | 99.82 | 0.1628 | 0.1616 | 0.1853 | RANDOM | 28.58 |
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] | |
2.8593 | 2.8593 | -5.7186 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 15.64 |
t_omega_torsion | 3.9 |
t_angle_deg | 1.09 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4348 |
Nucleic Acid Atoms | |
Solvent Atoms | 598 |
Heterogen Atoms | 113 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
PHASER | phasing |
PDB_EXTRACT | data extraction |