6FTB

Staphylococcus aureus monofunctional glycosyltransferase in complex with moenomycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HZS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6295SA MGT E100Q (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 MOENOMYCIN 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 295 K.
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
12.123.1299.90.17313.63.945531237.46
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)
12.12.21000.3813.23.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3HZS2.123.121908296399.80.1990.1970.237RANDOM42.1
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]
0.91410.9141-1.8282
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.19
t_omega_torsion3.11
t_angle_deg1.06
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.19
t_omega_torsion3.11
t_angle_deg1.06
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1713
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms216

Software

Software
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing