6WGY
Crystal structure of a Putative citrate synthase 2 from Mycobacterium bovis in complex with citrate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 290 | Micolytic MCSG-1 screen, condition D7: 20% (w/V) PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: MyboA.00896.a.AE1.PS38615 (originally labelled as MythA.10611.a.AE1.PS38615) at 34.35 mg/ml. For phasing the crystal was incubated for 20sec in a mix of 90% reservoir and 10% 2.5M NaI in ethylene glycol, followed by an incubation for 20sec in 80% reservoir and 20% 2.5M NaI in ethylene glycol. The sample was then vitirfied. tray 314035d7: cryo: 20% PEG with 2.5M NaI: puck dvf9-2. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.99 | 58.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.14 | α = 90 |
b = 153.37 | β = 90 |
c = 100.58 | 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 | RIGAKU SATURN 944+ | RIGAKU VARIMAX HF | 2020-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | 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 | 2.3 | 50 | 99.9 | 0.093 | 0.097 | 0.999 | 19.33 | 14.398 | 87868 | 46.634 |
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 | 2.3 | 2.36 | 99.8 | 0.64 | 0.663 | 0.956 | 5.07 | 14.528 |
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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | FREE R-VALUE | 2.3 | 47.43 | 1.3 | 87847 | 1950 | 99.94 | 0.1748 | 0.1737 | 0.2252 | 0 | 44.42 |
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 | 18.8812 |
f_angle_d | 0.8132 |
f_chiral_restr | 0.0473 |
f_bond_d | 0.0067 |
f_plane_restr | 0.0055 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11061 |
Nucleic Acid Atoms | |
Solvent Atoms | 802 |
Heterogen Atoms | 135 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
SHELXDE | phasing |
PHASER | phasing |
PARROT | phasing |
SHELXE | model building |
ARP/wARP | model building |
Coot | model building |