6GX0

Blood group synthase AAGlyB in complex with UDP-Gal and cryoprotected with PEG 3350


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293MOPS buffer, Magnesium chloride, ammonium sulfate and PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2745.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.849α = 90
b = 148.92β = 90
c = 80.039γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-08-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.072ESRFID29

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
11.2542.2999.90.093115.387298
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)
11.251.270.672

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 DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE3ZGG1.253082794446899.810.123330.121870.15081RANDOM13.364
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]
-0.170.43-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.922
r_sphericity_free21.672
r_dihedral_angle_4_deg18.796
r_dihedral_angle_3_deg11.557
r_dihedral_angle_1_deg6.573
r_sphericity_bonded6.211
r_long_range_B_refined2.55
r_long_range_B_other2.123
r_rigid_bond_restr1.905
r_scangle_other1.692
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.922
r_sphericity_free21.672
r_dihedral_angle_4_deg18.796
r_dihedral_angle_3_deg11.557
r_dihedral_angle_1_deg6.573
r_sphericity_bonded6.211
r_long_range_B_refined2.55
r_long_range_B_other2.123
r_rigid_bond_restr1.905
r_scangle_other1.692
r_angle_refined_deg1.666
r_scbond_it1.424
r_scbond_other1.423
r_mcangle_it1.264
r_mcangle_other1.264
r_mcbond_it1.015
r_mcbond_other1.015
r_angle_other_deg1.012
r_chiral_restr0.1
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2360
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing