3VBP

Crystal Structure of the D94N mutant of AntD, an N-acyltransferase from Bacillus cereus in complex with dTDP 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
2.5852.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.339α = 90
b = 71.339β = 90
c = 138.184γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Montel2011-08-22MSINGLE 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
12.340.74197.50.10.18.24.43073229979
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)
12.32.492.80.3110.3112.72.73122

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 MODEL2.340.7412995728459149897.60.192190.188730.25856RANDOM35.995
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]
-0.18-0.180.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.257
r_dihedral_angle_3_deg18.586
r_dihedral_angle_4_deg14.342
r_dihedral_angle_1_deg7.68
r_scangle_it5.093
r_scbond_it3.282
r_angle_refined_deg2.322
r_mcangle_it2.105
r_mcbond_it1.175
r_chiral_restr0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.257
r_dihedral_angle_3_deg18.586
r_dihedral_angle_4_deg14.342
r_dihedral_angle_1_deg7.68
r_scangle_it5.093
r_scbond_it3.282
r_angle_refined_deg2.322
r_mcangle_it2.105
r_mcbond_it1.175
r_chiral_restr0.154
r_bond_refined_d0.01
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4302
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms220

Software

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