6GX2

Blood group synthase AAGlyB in complex with UDP-GalNAc and cryoprotected with glycerol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZGG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293MOPS buffer, Magnesium chloride, ammonium sulfate and PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2545.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.569α = 90
b = 148.682β = 90
c = 79.677γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9762ESRFID23-1

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
11.0749.5699.20.0959.54.7135972
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)
11.071.090.71

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-VALUE3ZGG1.0740129085685799.090.112880.111780.13385RANDOM11.469
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]
-0.110.23-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.744
r_dihedral_angle_4_deg22.623
r_sphericity_free19.222
r_dihedral_angle_3_deg12.091
r_sphericity_bonded7.602
r_dihedral_angle_1_deg7.142
r_long_range_B_refined2.842
r_long_range_B_other2.471
r_rigid_bond_restr2.116
r_scangle_other2.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.744
r_dihedral_angle_4_deg22.623
r_sphericity_free19.222
r_dihedral_angle_3_deg12.091
r_sphericity_bonded7.602
r_dihedral_angle_1_deg7.142
r_long_range_B_refined2.842
r_long_range_B_other2.471
r_rigid_bond_restr2.116
r_scangle_other2.074
r_scbond_it1.782
r_scbond_other1.754
r_angle_refined_deg1.728
r_mcangle_other1.483
r_mcangle_it1.482
r_mcbond_it1.18
r_mcbond_other1.178
r_angle_other_deg1.115
r_chiral_restr0.111
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.001
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 Atoms2435
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing