3VBK

Crystal Structure of the S84A mutant of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP-4-amino-4,6-dideoxyglucose and Coenzyme A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherIN-HOUSE MIR MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629825% pentaerythritol ethoxylate (3/4 EO/OH), 2% isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5852.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.254α = 90
b = 71.254β = 90
c = 138.382γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Montel2011-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.240.7395.30.0550.05514.44.13509733434
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.386.70.1890.1893.123509

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIN-HOUSE MIR MODEL2.240.733342331748167595.360.187660.184360.24956RANDOM30.228
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]
0.230.23-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.525
r_dihedral_angle_3_deg18.286
r_dihedral_angle_4_deg17.143
r_dihedral_angle_1_deg7.774
r_scangle_it5.184
r_scbond_it3.522
r_angle_refined_deg2.276
r_mcangle_it2.171
r_mcbond_it1.304
r_chiral_restr0.168
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.525
r_dihedral_angle_3_deg18.286
r_dihedral_angle_4_deg17.143
r_dihedral_angle_1_deg7.774
r_scangle_it5.184
r_scbond_it3.522
r_angle_refined_deg2.276
r_mcangle_it2.171
r_mcbond_it1.304
r_chiral_restr0.168
r_bond_refined_d0.01
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4308
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms262

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling