3VFK

The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UBQPDB entry 1UBQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62910.1 M magnesium chloride, 0.1 M sodium acetate 4.6, 18% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
238.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.01α = 90
b = 25.18β = 109.18
c = 38.71γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 3152009-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.9792APS24-ID-E

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
12.819.29499.22084-3

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 1UBQ2.819.2942.0420849399.950.27890.27760.3057
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]
8.4159-18.7315-20.260111.8442
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.765
f_angle_d0.847
f_chiral_restr0.037
f_bond_d0.005
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms711
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms47

Software

Software
Software NamePurpose
MOLREPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling