1RJ8 | pdb_00001rj8

The crystal structure of TNF family member EDA-A2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		EDA-A1 trimer containing residues 248-307, 319-333, 347-390

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	0.2M NaCl, 0.1M Hepes, 25% Peg 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 19K

Crystal Properties
Matthews coefficient	Solvent content
1.9	30

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.723	α = 90
b = 161.337	β = 105.24
c = 51.023	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	100	IMAGE PLATE	MARRESEARCH	Osmic Mirrors	2003-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	96.8	0.03	0.043	23	2.7	38487	37259		-3	25

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	2.33	94.6		0.089	9.5	2.51	3698

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 (All)	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	EDA-A1 trimer containing residues 248-307, 319-333, 347-390	2.23	30	37233	33523	3700	97.25	0.2043	0.2043	0.20009	0.2	0.24052	0.24	THIN SHELLS	6.364

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]
0.26		0.55	-0.61		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	12.419
r_dihedral_angle_1_deg	6.762
r_scangle_it	2.644
r_mcangle_it	1.826
r_scbond_it	1.799
r_mcbond_it	1.189
r_angle_refined_deg	1.159
r_angle_other_deg	0.757
r_symmetry_vdw_refined	0.292
r_symmetry_vdw_other	0.286
r_nbd_other	0.243
r_nbd_refined	0.236
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.158
r_nbtor_other	0.08
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6594
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
AMoRE	phasing