8STD
S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate NaAD and soaked with CS2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7MJ2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 100 mM magnesium formate, 20% w/v PEG 3350, 2 mM nitrilotriacetic acid neutralized to a pH of ~7.5 with sodium hydroxide, and 0.7 mM zinc sulfate, 10 mM EDTA, 10 mM Nicotinic acid adenine dinucleotide sodium salt, soaked with ~10-15% Carbon disulfide for 20 minutes during freezing |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 118.839 | α = 90 |
b = 118.839 | β = 90 |
c = 211.289 | γ = 90 |
Symmetry | |
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Space Group | P 4 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 EIGER X 9M | 2022-11-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.5498 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.65 | 84.03 | 100 | 0.983 | 6.5 | 6.7 | 44856 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.65 | 2.75 | 0.38 | 1.1 |
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 | THROUGHOUT | 2.65 | 78.96 | 1.34 | 44538 | 2245 | 99.44 | 0.2434 | 0.2418 | 0.2728 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
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 | 13.588 |
f_angle_d | 1.002 |
f_chiral_restr | 0.051 |
f_bond_d | 0.018 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8360 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 219 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |