9IBF | pdb_00009ibf

Crystal structure of hFcgammaRI-FAb complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4W4O	Immunoglobulin gamma Fc receptor I
experimental model	PDB	1I8M	Antibody FAb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	MOPS/HEPES buffer pH 7.5 0.12 M alcohol mixture 30% PEG20k-PEG MME550 mixture

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.715	α = 90
b = 126.491	β = 90
c = 141.483	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X CdTe 9M		2024-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.61992	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	3.2	57.806	100	0.946	0.192	0.975	4.1	25.1		36765

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.34	100		4.17	0.855	0.515	1.2	25.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.2	57.7	36695	2083	99.946	0.262	0.2591	0.2694	0.314	0.326	Random	72.824

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]
-5.386			10.826		-5.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.812
r_lrange_it	14.732
r_dihedral_angle_6_deg	14.349
r_scangle_it	9.887
r_mcangle_it	8.556
r_dihedral_angle_2_deg	7.41
r_dihedral_angle_1_deg	6.991
r_scbond_it	6.104
r_mcbond_it	5.157
r_angle_refined_deg	1.775
r_symmetry_nbd_refined	0.406
r_nbtor_refined	0.315
r_nbd_refined	0.243
r_symmetry_xyhbond_nbd_refined	0.238
r_xyhbond_nbd_refined	0.211
r_chiral_restr	0.118
r_gen_planes_refined	0.01
r_bond_refined_d	0.007
r_ext_dist_refined_b	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10858
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	171

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building