5M7D

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293MOPS buffer, manganese chloride, ammonium sulfate, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2545.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.643α = 90
b = 148.796β = 90
c = 79.782γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-08-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.0723ESRFID29

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
11.242.1499.10.08810.43.596982
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)
11.21.2299.30.5222.13.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.24092055490098.980.131630.130330.15654RANDOM12.791
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]
-0.50.490.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.336
r_dihedral_angle_4_deg18.859
r_dihedral_angle_3_deg12.461
r_sphericity_bonded7.298
r_dihedral_angle_1_deg6.648
r_rigid_bond_restr4.942
r_sphericity_free4.072
r_long_range_B_refined2.554
r_long_range_B_other2.042
r_scangle_other2.025
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.336
r_dihedral_angle_4_deg18.859
r_dihedral_angle_3_deg12.461
r_sphericity_bonded7.298
r_dihedral_angle_1_deg6.648
r_rigid_bond_restr4.942
r_sphericity_free4.072
r_long_range_B_refined2.554
r_long_range_B_other2.042
r_scangle_other2.025
r_scbond_it1.887
r_scbond_other1.824
r_angle_refined_deg1.671
r_mcangle_other1.524
r_mcangle_it1.521
r_mcbond_it1.188
r_mcbond_other1.172
r_angle_other_deg0.987
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.009
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2427
Nucleic Acid Atoms
Solvent Atoms362
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing