Experiment: 1RJ8

X-RAY DIFFRACTION

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

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.