5AJP

Crystal structure of the active form of GalNAc-T2 in complex with UDP and the glycopeptide MUC5AC-13


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D0TPDB ENTRY 4D0T

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.5651.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.266α = 90
b = 87.266β = 90
c = 178.59γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.652099.80.0422.16.7797092
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)
11.651.7499.20.62.95.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4D0T1.6589.2977496218799.810.156820.155980.18558RANDOM28.104
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]
-0.75-0.751.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.46
r_dihedral_angle_4_deg18.211
r_dihedral_angle_3_deg13.11
r_dihedral_angle_1_deg6.36
r_scbond_it2.82
r_mcangle_it2.393
r_mcbond_it1.632
r_mcbond_other1.631
r_angle_refined_deg1.627
r_angle_other_deg0.831
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.46
r_dihedral_angle_4_deg18.211
r_dihedral_angle_3_deg13.11
r_dihedral_angle_1_deg6.36
r_scbond_it2.82
r_mcangle_it2.393
r_mcbond_it1.632
r_mcbond_other1.631
r_angle_refined_deg1.627
r_angle_other_deg0.831
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.008
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4061
Nucleic Acid Atoms
Solvent Atoms611
Heterogen Atoms145

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing