6YAX

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OCC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.2 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 coefficient	Solvent content
3.2	61.53

Crystal Data

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

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 4M		2017-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.97	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.8	47.86	99.3	0.995	9.1	7.2		41024

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.87			0.491

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5OCC	2.8	47.86	40956	1971	99.555	0.232	0.2299	0.2644	70.396

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]
0.214			0.214		-0.427

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.877
r_dihedral_angle_4_deg	18.786
r_dihedral_angle_3_deg	15.811
r_dihedral_angle_1_deg	7.554
r_lrange_it	7.215
r_lrange_other	7.215
r_scangle_it	5.041
r_scangle_other	5.04
r_mcangle_it	4.768
r_mcangle_other	4.768
r_scbond_it	3.187
r_scbond_other	3.187
r_mcbond_it	3.042
r_mcbond_other	3.042
r_angle_other_deg	2.427
r_angle_refined_deg	1.383
r_symmetry_xyhbond_nbd_refined	0.253
r_symmetry_nbd_refined	0.231
r_nbd_other	0.23
r_symmetry_nbd_other	0.221
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.158
r_symmetry_xyhbond_nbd_other	0.126
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.049
r_bond_other_d	0.036
r_gen_planes_other	0.007
r_bond_refined_d	0.004
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8293
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing