3WAG | pdb_00003wag

Crystal structure of glycosyltransferase VinC in complex with DTDP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529320 %(W/V) PEG 3350, 0.2M MGCL2, 100MM TRIS, 10MM DTDP, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.829α = 90
b = 130.162β = 90
c = 139.787γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102007-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0SPring-8BL26B1

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
12.150935257548895
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1874.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3WAD2.131.754642746427246792.80.1940.1940.1910.190.2560.26RANDOM42.18
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]
-0.040.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.9
r_dihedral_angle_4_deg19.335
r_dihedral_angle_3_deg18.402
r_dihedral_angle_1_deg6.92
r_angle_refined_deg2.029
r_chiral_restr0.124
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6191
Nucleic Acid Atoms
Solvent Atoms372
Heterogen Atoms66

Software

Software
Software NamePurpose
BSSdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing