7S3U

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MZU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829316-20% PEG-3350, 200 mM KCl, 5 mM dTDP-3-amino-3,6-dideoxy-D-glucose, 5 mM Coenzyme A, 100 mM HEPPS
Crystal Properties
Matthews coefficientSolvent content
2.5150.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.97α = 90
b = 102.97β = 90
c = 102.97γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2020-08-27MSINGLE 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
11.455099.80.04418.714.332307
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)
11.4561.55990.2145.18.8

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 REPLACEMENTTHROUGHOUT4mzu1.4536.4330754155399.790.17260.17170.1921RANDOM11.482
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_deg25.348
r_dihedral_angle_2_deg24.112
r_dihedral_angle_3_deg12.972
r_dihedral_angle_1_deg7.501
r_angle_refined_deg1.643
r_angle_other_deg1.354
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg25.348
r_dihedral_angle_2_deg24.112
r_dihedral_angle_3_deg12.972
r_dihedral_angle_1_deg7.501
r_angle_refined_deg1.643
r_angle_other_deg1.354
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1107
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing