2FYB

Crystal structure of the catalytic domain of the human beta1,4-galactosyltransferase mutant M339H in complex with Mn and UDP-galactose in open conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FY7PDB ENTRY 2FY7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.629810 mg/ml protein solution, 5mM manganese chloride, 5mM UDP-galactose, 50 mM sodium citrate, 6% PEG 4000, pH 5.6, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4650.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.56α = 90
b = 137.73β = 90
c = 66.43γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHmirrors2002-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.852097.10.056224.1527622120
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.851.92920.3813.32585

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 2FY71.919.7925263251797.60.1780.1780.216RANDOM26.1
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]
2.11-3.681.57
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.9
c_scangle_it3.05
c_scbond_it2.13
c_mcangle_it1.98
c_angle_deg1.7
c_mcbond_it1.33
c_improper_angle_d1.07
c_bond_d0.014
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.9
c_scangle_it3.05
c_scbond_it2.13
c_mcangle_it1.98
c_angle_deg1.7
c_mcbond_it1.33
c_improper_angle_d1.07
c_bond_d0.014
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2194
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms26

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing