6GX1

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293MOPS buffer, Magnesium sulfate, ammonium sulfate and PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2545.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.635α = 90
b = 148.386β = 90
c = 79.816γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-04-02MSINGLE 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
11.642.131000.10112.46.541668
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.63

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-VALUE3ZGG1.64039486216099.910.16480.163070.19775RANDOM15.854
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]
-0.991.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.118
r_dihedral_angle_4_deg14.134
r_dihedral_angle_3_deg12.423
r_dihedral_angle_1_deg6.356
r_long_range_B_refined4.112
r_long_range_B_other3.819
r_scangle_other2.238
r_angle_refined_deg1.535
r_mcangle_it1.487
r_mcangle_other1.486
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.118
r_dihedral_angle_4_deg14.134
r_dihedral_angle_3_deg12.423
r_dihedral_angle_1_deg6.356
r_long_range_B_refined4.112
r_long_range_B_other3.819
r_scangle_other2.238
r_angle_refined_deg1.535
r_mcangle_it1.487
r_mcangle_other1.486
r_scbond_it1.381
r_scbond_other1.381
r_mcbond_it0.971
r_mcbond_other0.959
r_angle_other_deg0.947
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2343
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing