5AJN

Crystal structure of the inactive form of GalNAc-T2 in complex with the glycopeptide MUC5AC-Cys13


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.5752.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.351α = 90
b = 87.351β = 90
c = 178.433γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOCALBAXALOC

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
11.672099.80.111.38.9769472
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)
11.671.761000.6539.2

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 4D0T1.6778.4573949209298.650.196660.195630.23216RANDOM23.836
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]
-0.17-0.170.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.162
r_dihedral_angle_4_deg15.975
r_dihedral_angle_3_deg13.774
r_dihedral_angle_1_deg6.79
r_scbond_it2.696
r_mcangle_it2.181
r_angle_refined_deg2.027
r_mcbond_it1.508
r_mcbond_other1.508
r_angle_other_deg0.942
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.162
r_dihedral_angle_4_deg15.975
r_dihedral_angle_3_deg13.774
r_dihedral_angle_1_deg6.79
r_scbond_it2.696
r_mcangle_it2.181
r_angle_refined_deg2.027
r_mcbond_it1.508
r_mcbond_other1.508
r_angle_other_deg0.942
r_chiral_restr0.124
r_bond_refined_d0.019
r_gen_planes_refined0.011
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 Atoms4064
Nucleic Acid Atoms
Solvent Atoms555
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing