6MQH
Crystal structure of 4-hydroxy-tetrahydrodipicolinate synthase (HTPA synthase) from Burkholderia mallei
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | 23.87 mg/mL BumaA.01563.a.B1.PW38480 + 5 mM AMPPNP + 5 mM magnesium chloride against Molecular Dimensions Morpheus screen, E3 (10% w/v PEG4000, 20% v/v glycerol, 30 mM diethyleneglycol, 30 mM triethyleneglycol, 30 mM tetraethyleneglycol, 30 mM pentaethyleneglycol, 100 mM MES/imidazole, pH 6.5), cryoprotecion: direct, tray 301751e3, puck egq4-8, for phasing, a crystal from an apo setup of the same protein from Rigaku Reagents JCSG+ screen C4 (10% PEG6000, 100 mM HEPES free acid/NaOH) was incubated for 10 seconds each in 12.5% 2.5 M sodium iodide in ethylene glycol and in 25% 2.5 M sodium iodide in ethylene glycol (625 mM final sodium iodide concentration) and directly vitrified, puck: OVZ1-3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 150.87 | α = 90 |
b = 53.93 | β = 90 |
c = 78.63 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | RAYONIX MX-300 | 2018-08-08 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | RIGAKU VARIMAX | 2018-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.7 | 44.474 | 99.5 | 0.061 | 0.067 | 0.999 | 19.01 | 6.081 | 71091 | 25.072 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.7 | 1.74 | 100 | 0.482 | 0.526 | 0.915 | 3.99 | 6.157 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 | THROUGHOUT | 1.7 | 44.474 | 1.34 | 70904 | 1957 | 99.23 | 0.1683 | 0.1675 | 0.1948 | 21.7755 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.457 |
f_angle_d | 0.95 |
f_chiral_restr | 0.063 |
f_bond_d | 0.008 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4340 |
Nucleic Acid Atoms | |
Solvent Atoms | 805 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
ARP/wARP | model building |
Coot | model building |
PHENIX | refinement |
PDB_EXTRACT | data extraction |