3HZS

S. aureus monofunctional glycosyltransferase (MtgA)in complex with moenomycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherUnpublished apo structure of MTGA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6295Sa MtgA E100Q at 10 mg/ml was mixed with 1mM Moenomycin and 1mM MnCl2 and incubated on ice for ~3 hours. Precipitated material was removed by centrifugation at 16,000xg for 5 minutes. The Mmoenomycin complex was crystallized by hanging drop vapor diffusion, mixing the protein 1:1 with a reservoir solution containing 0.1M Na Acetate pH 4.6, 0.2M NaCl, 30% MPD at 22oC. Hexagonal plate crystals formed in 1 week., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.3563.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.422α = 90
b = 114.422β = 90
c = 128.844γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944Rigaku Varimax HF optics2007-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.54

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
12.123.1299.90.17313.63.94553122
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)
12.12.21000.3813.23.84606

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTUnpublished apo structure of MTGA2.123.1222455311812196399.690.191830.189170.24379RANDOM36.033
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]
-2.03-1.02-2.033.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.965
r_dihedral_angle_4_deg21.85
r_dihedral_angle_3_deg14.695
r_scangle_it7.279
r_dihedral_angle_1_deg5.865
r_scbond_it5.623
r_mcangle_it3.675
r_mcbond_it2.401
r_angle_refined_deg1.8
r_chiral_restr0.169
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.965
r_dihedral_angle_4_deg21.85
r_dihedral_angle_3_deg14.695
r_scangle_it7.279
r_dihedral_angle_1_deg5.865
r_scbond_it5.623
r_mcangle_it3.675
r_mcbond_it2.401
r_angle_refined_deg1.8
r_chiral_restr0.169
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1708
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms105

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling