5NQA

Crystal structure of GalNAc-T4 in complex with the monoglycopeptide 3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PEG3350, ammonium nitrate
Crystal Properties
Matthews coefficientSolvent content
2.8757.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.447α = 116.47
b = 79.881β = 96.74
c = 88.614γ = 104.72
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97DiamondI03

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
11.976.4597.50.0680.9886.93.6115064
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9295.80.5563.2

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 REPLACEMENTTHROUGHOUT5AJP1.976.45111879318297.470.225940.224590.27393RANDOM33.271
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]
-0.27-0.87-0.62-0.790.530.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.779
r_dihedral_angle_4_deg16.064
r_dihedral_angle_3_deg15.744
r_dihedral_angle_1_deg6.788
r_long_range_B_refined5.521
r_long_range_B_other5.521
r_scangle_other2.328
r_mcangle_other2.218
r_mcangle_it2.217
r_angle_refined_deg1.718
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.779
r_dihedral_angle_4_deg16.064
r_dihedral_angle_3_deg15.744
r_dihedral_angle_1_deg6.788
r_long_range_B_refined5.521
r_long_range_B_other5.521
r_scangle_other2.328
r_mcangle_other2.218
r_mcangle_it2.217
r_angle_refined_deg1.718
r_scbond_it1.513
r_scbond_other1.513
r_mcbond_it1.381
r_mcbond_other1.379
r_angle_other_deg1.051
r_chiral_restr0.107
r_bond_refined_d0.014
r_gen_planes_refined0.008
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 Atoms8405
Nucleic Acid Atoms
Solvent Atoms1567
Heterogen Atoms373

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing