4Q38

The crystal structure of acyltransferase in complex with decanoyl-CoA and teicoplanin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1mM MES, 0.2M ammonium sulphate, 30%(V/V) PEG 5000 MME, 1mM decanoyl-CoA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3162.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.806α = 90
b = 133.806β = 90
c = 49.301γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2014-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A1.0000NSRRCBL15A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.993099.8346063460622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0799.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4MFJ1.9922.523284932849174199.710.193160.193160.191740.22033RANDOM34.49
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]
-0.35-0.17-0.350.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.599
r_dihedral_angle_4_deg15.62
r_dihedral_angle_3_deg13.475
r_dihedral_angle_1_deg5.028
r_angle_refined_deg1.181
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2607
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms81

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling