4F78

Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.32980.2 M ammonium sulfate, 0.1 M sodium cacodylate, 30% PEG 8K, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2745.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.912α = 90
b = 43.96β = 99.19
c = 80.199γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2011-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97918APS21-ID-D

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
11.9579.171000.07810.63.319747-3
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)
11.952.061000.3293.63.32850

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.9539.5841.351973494998.350.15540.15360.1864random
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]
-1.7143-4.27791.34940.3648
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.268
f_angle_d1.494
f_chiral_restr0.116
f_bond_d0.016
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2054
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms65

Software

Software
Software NamePurpose
HKL-3000data collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing