6YAX

Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M 1,2-propanediol, 0.2 M 2- propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 1.0 M tris (base), BICINE, 40% v/v PEG 500 MME, 20% w/v PEG 20000
Crystal Properties
Matthews coefficientSolvent content
3.261.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.728α = 90
b = 95.728β = 90
c = 186.038γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2017-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.97ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.847.8699.30.9959.17.241024
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.870.491

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5OCC2.847.8640956197199.5550.2320.22990.264470.396
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]
0.2140.214-0.427
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.877
r_dihedral_angle_4_deg18.786
r_dihedral_angle_3_deg15.811
r_dihedral_angle_1_deg7.554
r_lrange_it7.215
r_lrange_other7.215
r_scangle_it5.041
r_scangle_other5.04
r_mcangle_it4.768
r_mcangle_other4.768
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.877
r_dihedral_angle_4_deg18.786
r_dihedral_angle_3_deg15.811
r_dihedral_angle_1_deg7.554
r_lrange_it7.215
r_lrange_other7.215
r_scangle_it5.041
r_scangle_other5.04
r_mcangle_it4.768
r_mcangle_other4.768
r_scbond_it3.187
r_scbond_other3.187
r_mcbond_it3.042
r_mcbond_other3.042
r_angle_other_deg2.427
r_angle_refined_deg1.383
r_symmetry_xyhbond_nbd_refined0.253
r_symmetry_nbd_refined0.231
r_nbd_other0.23
r_symmetry_nbd_other0.221
r_nbd_refined0.193
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.158
r_symmetry_xyhbond_nbd_other0.126
r_symmetry_nbtor_other0.086
r_chiral_restr0.049
r_bond_other_d0.036
r_gen_planes_other0.007
r_bond_refined_d0.004
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8293
Nucleic Acid Atoms
Solvent Atoms277
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing