6V91
Crystal structure of Stringent starvation protein A (BTH_I2974) from Burkholderia thailandensis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 290 | For native data collection: Anatrace Morpheus screen G7: 20mM of each Sodium formate, Ammonium acetate, Sodium citrate tribasic dihydrate, Sodium potassium tartrate tetrahydrate, Sodium oxamate: 100mM Na-HEPES / MOPS acid pH 7.5: 40% (V/V) Glycerol, 20% (w/V) PEG 4000: ButhA.17888.a.AE1 (labled as CrpaA.01056.a.AE1.PW38685) at 30.5mg/ml: 311984 g7: cryo: direct: puck ocs5-5. For phasing, a crystal from the same tray, condition H9 (20mM of each L-Na-Glutamate, Alanine (racemic), Glycine, Lysine HCl (racemic), Serine (racemic): 100mM Tris base / Bicine pH 8.5: 40% (v/v) PEG 500 MME, 20% (w/V) PEG 20000) was incubated for 30sec in a mix of 90% reservoir and 10% 5M NaI in ethylene glycol and vitrified without further cryoprotection. 360deg of data were collected in-house at Cu-Ka radiation.Tray: 311984 h9, puck ocs5-14. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.38 | α = 90 |
b = 95.64 | β = 90 |
c = 108.85 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2019-11-21 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2019-11-22 | 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 | 1.9 | 50 | 99.5 | 0.047 | 0.051 | 0.999 | 19.65 | 5.952 | 50160 | 40.249 |
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 | 1.9 | 1.95 | 96.9 | 0.52 | 0.57 | 0.909 | 3.58 | 6.006 |
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 | 1.9 | 33.92 | 1.34 | 50149 | 2022 | 99.46 | 0.1756 | 0.174 | 0.2149 | 0 | 49.18 |
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 | 20.4957 |
f_angle_d | 0.852 |
f_chiral_restr | 0.0532 |
f_bond_d | 0.0068 |
f_plane_restr | 0.0058 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3298 |
Nucleic Acid Atoms | |
Solvent Atoms | 307 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |