3HA0 | pdb_00003ha0

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	PDB	1FP5	PDB entry 1FP5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.3	293	0.5 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 0.5 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
2.56	51.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.9	α = 90
b = 104.9	β = 96.2
c = 150	γ = 90

Symmetry
Space Group	P 1 21 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		1999-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.0001	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	2.8	30	99.9	0.073	16.7	3.7	37208	37208

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	2.8	2.9	100		0.541		3.4

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	PDB entry 1FP5	2.8	29.83	36905	36845	1860	100	0.24339	0.24144	0.25	0.28015	0.29	RANDOM	63.102

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]
-1.73		-0.56	1.53		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.105
r_dihedral_angle_3_deg	12.064
r_dihedral_angle_4_deg	10.085
r_dihedral_angle_1_deg	4.339
r_mcangle_it	1.182
r_angle_refined_deg	0.908
r_scangle_it	0.816
r_mcbond_it	0.672
r_angle_other_deg	0.616
r_scbond_it	0.477
r_mcbond_other	0.071
r_chiral_restr	0.053
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other
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	9910
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	366

Software

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