5XJE | pdb_00005xje

Crystal structure of fucosylated IgG1 Fc complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AY4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529312% PEG 20000, 0.1 M MES (pH 6.5), 4% Zwittergent 3-12
Crystal Properties
Matthews coefficientSolvent content
3.7366.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.55α = 90
b = 77.55β = 90
c = 351.89γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2012-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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
12.446.7899.50.10414.211.243217
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)
12.42.5497.10.6111.65.6

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 REPLACEMENTTHROUGHOUT3AY42.42040966215699.290.235140.232750.240.28070.28RANDOM55.114
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]
0.430.43-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.335
r_dihedral_angle_3_deg16.381
r_dihedral_angle_4_deg13.367
r_long_range_B_refined7.497
r_long_range_B_other7.497
r_dihedral_angle_1_deg6.599
r_scangle_other5.428
r_mcangle_it4.962
r_mcangle_other4.962
r_scbond_it3.397
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.335
r_dihedral_angle_3_deg16.381
r_dihedral_angle_4_deg13.367
r_long_range_B_refined7.497
r_long_range_B_other7.497
r_dihedral_angle_1_deg6.599
r_scangle_other5.428
r_mcangle_it4.962
r_mcangle_other4.962
r_scbond_it3.397
r_scbond_other3.394
r_mcbond_it3.157
r_mcbond_other3.157
r_angle_refined_deg1.573
r_angle_other_deg0.937
r_chiral_restr0.181
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms4637
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms284

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing