3VBN

Crystal Structure of the D94A 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
2.5551.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.076α = 90
b = 71.076β = 90
c = 137.749γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135Montel2011-08-29MSINGLE 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
12.540.59994.40.1510.1515.942381322486
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)
12.52.680.70.380.381.61.42201

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 MODEL2.540.5992245821291116794.450.199930.195740.27688RANDOM28.836
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]
-0.31-0.310.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.019
r_dihedral_angle_3_deg20.148
r_dihedral_angle_4_deg17.992
r_dihedral_angle_1_deg7.687
r_scangle_it3.699
r_scbond_it2.27
r_angle_refined_deg2.211
r_mcangle_it1.561
r_mcbond_it0.835
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.019
r_dihedral_angle_3_deg20.148
r_dihedral_angle_4_deg17.992
r_dihedral_angle_1_deg7.687
r_scangle_it3.699
r_scbond_it2.27
r_angle_refined_deg2.211
r_mcangle_it1.561
r_mcbond_it0.835
r_chiral_restr0.135
r_bond_refined_d0.011
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4309
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms220

Software

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