2VS5

THE BINDING OF UDP-GALACTOSE BY AN ACTIVE SITE MUTANT OF alpha-1,3 GALACTOSYLTRANSFERASE (alpha3GT)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K4VPDB ENTRY 1K4V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16PROTEIN: 10 % GLYCEROL, 20 MM MES-NAOH PH 6.0, 10 MM MNCL2, 10 MM UDP-GAL, MOTHER LIQUOR: 10 % PEG 6000, 0.1 M TRIS-HCL PH 8.0, 8 % MPD
Crystal Properties
Matthews coefficientSolvent content
2.855.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.027α = 90
b = 91.37β = 90
c = 94.63γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2005-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
11.825097.90.17.86.46839413.4
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)
11.821.8997.90.522.5

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 1K4V1.8224.5751818625775.90.2360.2360.242RANDOM18.8
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]
-0.484.65-4.17
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.7
c_angle_deg1.3
c_improper_angle_d0.81
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.7
c_angle_deg1.3
c_improper_angle_d0.81
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4640
Nucleic Acid Atoms
Solvent Atoms723
Heterogen Atoms83

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing