7S41

Crystal structure of an N-acetyltransferase from Helicobacter pullorum in the presence of Coenzyme A and dTDP-3-acetamido-3,6-dideoxy-D-glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7S3U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529315% PEG-5000, 5 mM dTDP-3-amino-3,6-dideoxy-D-glucose, 5 mM coenzyme A, 100 mM HEPES. Crystals were harvested and soaked in 20% PEG-5000, 200 mM NaCl, 5 mM dTDP-3-amino-3,6-dideoxy-D-glucose, 5 mM acetyl coenzyme A, 100 mM HEPES
Crystal Properties
Matthews coefficientSolvent content
2.4148.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.965α = 90
b = 102.965β = 90
c = 102.965γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2020-09-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4501000.0414.517.135803
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.599.90.2344.511.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7s3u1.436.4334048175599.970.16380.16280.1826RANDOM12.433
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
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg25.917
r_dihedral_angle_2_deg25.889
r_dihedral_angle_3_deg12.744
r_dihedral_angle_1_deg8.062
r_angle_refined_deg1.687
r_angle_other_deg1.376
r_chiral_restr0.38
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg25.917
r_dihedral_angle_2_deg25.889
r_dihedral_angle_3_deg12.744
r_dihedral_angle_1_deg8.062
r_angle_refined_deg1.687
r_angle_other_deg1.376
r_chiral_restr0.38
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1155
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling
REFMACphasing