3LW6

Crystal Structure of Drosophila beta1,4-galactosyltransferase-7


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherBrominated structure was solved using SAD at 2.0 A resolution and the cordinated are used as the stating model.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829810-20 mg/ml protein with 33 mm UDP and 66 mM MnCl2 with a precipitation solution containing 100 mM Tris.HCl, 1 M NaCl, 15% MPD and 5% PEG 4K., pH 8.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3663.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.835α = 90
b = 81.835β = 90
c = 133.656γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2009-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.8150980.0633511.9413214132111
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)
1.811.87850.4134.29.91669

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTBrominated structure was solved using SAD at 2.0 A resolution and the cordinated are used as the stating model.1.8136.63911439114207997.830.190290.188710.22059RANDOM
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.158
r_dihedral_angle_4_deg12.884
r_dihedral_angle_3_deg12.172
r_dihedral_angle_1_deg6.738
r_scangle_it5.105
r_scbond_it3.405
r_mcangle_it2.127
r_angle_refined_deg1.991
r_mcbond_it1.212
r_chiral_restr0.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.158
r_dihedral_angle_4_deg12.884
r_dihedral_angle_3_deg12.172
r_dihedral_angle_1_deg6.738
r_scangle_it5.105
r_scbond_it3.405
r_mcangle_it2.127
r_angle_refined_deg1.991
r_mcbond_it1.212
r_chiral_restr0.163
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1997
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms34

Software

Software
Software NamePurpose
HKL-3000data collection
SHELXSphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling