3H9Y | pdb_00003h9y

Crystal structure of the IgE-Fc3-4 domains

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Partially-refined monomer (chain C) from the IgE-Fc3-4 carbohydrate mutant P21 crystal form.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.3	293	1 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 1 microliter well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.676	α = 90
b = 104.994	β = 101.61
c = 49.222	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	CCD	MAR CCD 130 mm		1998-08-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.00796	APS	5ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.23	30	98.8	0.061	20.943	3.8	36675	36675

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.23	2.38	89.8		0.513		3.45

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Partially-refined monomer (chain C) from the IgE-Fc3-4 carbohydrate mutant P21 crystal form.	2.23	29.64	36671	36671	1866	97.91	0.23263	0.23101	0.23	0.26212	0.26	RANDOM	37.9

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]
-0.18		-0.08	0.86		-0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.499
r_dihedral_angle_4_deg	13.432
r_dihedral_angle_3_deg	12.737
r_dihedral_angle_1_deg	5.57
r_mcangle_it	1.928
r_scangle_it	1.621
r_angle_refined_deg	1.232
r_mcbond_it	1.153
r_scbond_it	1.049
r_angle_other_deg	0.752
r_mcbond_other	0.199
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4968
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	195

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection