Experiment: 3B93

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.2M Lithium sulfate, 0.1M Tris, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.413	α = 90
b = 46.384	β = 91.56
c = 76.46	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	100	IMAGE PLATE	RIGAKU RAXIS IV		2006-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	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	2.2	75	96.9	0.08	0.08	127.9	5	16716	16198	5	3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	87.8		0.547	0.547	5.8	3.5	1627

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	mouse GITRL	2.2	75	16716	16198	1012	90.76	0.20872	0.20394	0.27992	RANDOM	42.022

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]
-1.68		-0.38	2.71		-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.06
r_dihedral_angle_3_deg	21.583
r_dihedral_angle_4_deg	13.064
r_dihedral_angle_1_deg	10.364
r_scangle_it	4.256
r_scbond_it	3.067
r_angle_refined_deg	2.521
r_mcangle_it	2.091
r_mcbond_it	1.347
r_nbtor_refined	0.326

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.06
r_dihedral_angle_3_deg	21.583
r_dihedral_angle_4_deg	13.064
r_dihedral_angle_1_deg	10.364
r_scangle_it	4.256
r_scbond_it	3.067
r_angle_refined_deg	2.521
r_mcangle_it	2.091
r_mcbond_it	1.347
r_nbtor_refined	0.326
r_nbd_refined	0.266
r_symmetry_vdw_refined	0.239
r_xyhbond_nbd_refined	0.219
r_symmetry_hbond_refined	0.182
r_chiral_restr	0.18
r_bond_refined_d	0.025
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2515
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement

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 R01GM133198.