2WGZ

Crystal structure of alpha-1,3 galactosyltransferase (alpha3GT) in a complex with p-nitrophenyl-beta-galactoside (pNP-beta-Gal)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
185% PEG 6000, 0.1M TRIS-HCL, PH 8.0 IN THE PRESENCE OF 10MM MNCL2 AND 10MM UDP
Crystal Properties
Matthews coefficientSolvent content
2.943

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.146α = 90
b = 94.222β = 99.05
c = 94.465γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2006-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.1SRSPX14.1

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
12.125094.40.0912.43.14457822.9
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)
12.122.280.70.225.143

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 1K4V2.1225.2940981107794.60.169590.168650.20582RANDOM18.96
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.23
r_dihedral_angle_4_deg16.659
r_dihedral_angle_3_deg13.525
r_dihedral_angle_1_deg5.749
r_angle_other_deg1.481
r_scangle_it1.435
r_angle_refined_deg1.001
r_scbond_it0.885
r_mcangle_it0.649
r_mcbond_it0.372
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.23
r_dihedral_angle_4_deg16.659
r_dihedral_angle_3_deg13.525
r_dihedral_angle_1_deg5.749
r_angle_other_deg1.481
r_scangle_it1.435
r_angle_refined_deg1.001
r_scbond_it0.885
r_mcangle_it0.649
r_mcbond_it0.372
r_nbtor_refined0.303
r_xyhbond_nbd_refined0.204
r_nbd_refined0.172
r_symmetry_vdw_refined0.124
r_symmetry_hbond_refined0.084
r_chiral_restr0.073
r_bond_other_d0.015
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4784
Nucleic Acid Atoms
Solvent Atoms549
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing