4EEC

Crystal Structure of the glycopeptide antibiotic sulfotransferase StaL complexed with A3P and desulfo-A47934.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OVFPDB ENTRY 2OVF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microbatch, under oil8.52950.5M LiCl, 0.1M Tris pH 8.5, 28% PEG-6K, microbatch, under oil, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0941.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.442α = 90
b = 82.583β = 90
c = 123.076γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002011-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.75099.90.07613.25.915536
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.751000.5965.8767

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2OVF2.7501543477399.360.22520.22270.2722RANDOM65.292
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]
8.07-0.52-7.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.851
r_dihedral_angle_4_deg25.181
r_dihedral_angle_3_deg21.314
r_dihedral_angle_1_deg6.746
r_scangle_it3.214
r_scbond_it1.937
r_angle_refined_deg1.661
r_mcangle_it1.322
r_mcbond_it0.72
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.851
r_dihedral_angle_4_deg25.181
r_dihedral_angle_3_deg21.314
r_dihedral_angle_1_deg6.746
r_scangle_it3.214
r_scbond_it1.937
r_angle_refined_deg1.661
r_mcangle_it1.322
r_mcbond_it0.72
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3862
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms27

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing