6S24

Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and the peptide 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NQA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291Morpheus precipitant mix 4, nitrate phosphate buffer and Morpheus buffer System 1
Crystal Properties
Matthews coefficientSolvent content
2.5652.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.655α = 90
b = 104.661β = 90
c = 143.186γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.97DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
12.1220940.0510.9967.75.341413
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.122.2371.90.4910.5221.23.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5NQA2.1219.9639661165193.750.193020.191190.23738RANDOM41.609
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]
-1.18-0.842.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.209
r_dihedral_angle_4_deg21.001
r_dihedral_angle_3_deg17.054
r_long_range_B_refined8.955
r_long_range_B_other8.933
r_dihedral_angle_1_deg7.826
r_scangle_other6.278
r_mcangle_it5.675
r_mcangle_other5.674
r_scbond_it4.421
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.209
r_dihedral_angle_4_deg21.001
r_dihedral_angle_3_deg17.054
r_long_range_B_refined8.955
r_long_range_B_other8.933
r_dihedral_angle_1_deg7.826
r_scangle_other6.278
r_mcangle_it5.675
r_mcangle_other5.674
r_scbond_it4.421
r_scbond_other4.046
r_mcbond_it3.708
r_mcbond_other3.706
r_angle_refined_deg1.688
r_angle_other_deg1.267
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4410
Nucleic Acid Atoms40
Solvent Atoms201
Heterogen Atoms105

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing