3B9I | pdb_00003b9i

Crystal Structure of mouse GITRL at 2.5 A.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QDN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	30% Pentaerythritol Ethoxylate(15/4 EO/OH), 0.05M Ammonium Sulfate and 0.05M Bis-Tris (pH 6.5), Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.791	α = 90
b = 70.024	β = 90
c = 71.654	γ = 90

Symmetry
Space Group	P 21 21 21

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		2007-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	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	2.49	50	99.2	0.14	0.108	5.9	5.1	9637	9637

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)
	2.49	2.59	98.4		0.525	0.487	3.2	5.3	923

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		THROUGHOUT	2QDN	2.49	30	9608	9608	463	98.86	0.189	0.189	0.186	0.1839	0.248	0.2451	RANDOM	23.445

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]
-0.59			0.03		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.786
r_dihedral_angle_3_deg	16.315
r_dihedral_angle_1_deg	6.693
r_scangle_it	3.439
r_mcangle_it	3.212
r_scbond_it	2.361
r_mcbond_it	2.142
r_angle_refined_deg	1.326
r_nbtor_refined	0.325
r_symmetry_hbond_refined	0.292
r_xyhbond_nbd_refined	0.203
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.144
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1982
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing