5VU0 | pdb_00005vu0

Crystal structure of the complex between afucosylated/galactosylated human IgG1 Fc and Fc gamma receptor IIIa (CD16A) with Man5 N-glycans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L6X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293100 mM Bis-Tris Propane pH 7.5, 16% PEG 20k, 100 mM Potassium thiocyanate, Cryo protection - 20% Ethylene Glycol
Crystal Properties
Matthews coefficientSolvent content
2.9558.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.069α = 90
b = 48.846β = 103.77
c = 134.927γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0APS23-ID-B

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
12.26131.0598.520.09313.39436958
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)
12.262.33696.720.68412.13.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1L6X2.261034512197597.290.194180.191670.20.237310.24RANDOM47.184
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]
-2.890.94-0.612.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.711
r_dihedral_angle_4_deg17.365
r_dihedral_angle_3_deg15.958
r_dihedral_angle_1_deg7.237
r_long_range_B_refined5.886
r_long_range_B_other5.884
r_scangle_other3.511
r_mcangle_it3.148
r_mcangle_other3.148
r_scbond_it2.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.711
r_dihedral_angle_4_deg17.365
r_dihedral_angle_3_deg15.958
r_dihedral_angle_1_deg7.237
r_long_range_B_refined5.886
r_long_range_B_other5.884
r_scangle_other3.511
r_mcangle_it3.148
r_mcangle_other3.148
r_scbond_it2.133
r_scbond_other2.131
r_angle_refined_deg2.037
r_mcbond_it1.882
r_mcbond_other1.88
r_angle_other_deg1.078
r_chiral_restr0.108
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.003
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 Atoms4732
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms281

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing