8U2V
Crystal Structure of methylglyoxal synthase from Borrelia burgdorferi
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 291 | Morpheus Fusion D7: 20% (v/v) Ethylene glycol; 10% (w/v) PEG 8000, 0.05M Tris (base); 0.05M BICINE pH 8.5, 0.01M Sodium fluoride, 0.01M Sodium bromide, 0.01M Sodium iodide, 0.2 M xylitol, 0.02 M D-{-)-fructose, 0.02 M D-sorbitol, 0.02 M myo-inositol, 0.02 M L-rhamnose monohydrate. BobuA.00692.a.A1.PB00123 at 15 mg/mL. plate 13451 well D7 drop1. Puck: PSL-0612, Cryo: direct. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.87 | 57.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 110.866 | α = 90 |
b = 110.866 | β = 90 |
c = 91.256 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | PIXEL | DECTRIS EIGER2 XE 9M | 2023-08-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.9795 | NSLS-II | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 2.5 | 49.58 | 100 | 0.15 | 0.153 | 0.032 | 1 | 17 | 23.8 | 20304 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.5 | 2.6 | 100 | 2.994 | 3.055 | 0.601 | 0.771 | 25.5 |
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 | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.5 | 34.25 | 1.33 | 20222 | 988 | 99.87 | 0.1998 | 0.198 | 0.2357 |
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 | 13.321 |
f_angle_d | 0.556 |
f_chiral_restr | 0.045 |
f_bond_d | 0.006 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2948 |
Nucleic Acid Atoms | |
Solvent Atoms | 14 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |