3B94 | pdb_00003b94

Crystal structure of human GITRL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		humane GITRL from C2 spacegroup

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.943	α = 90
b = 141.943	β = 90
c = 47.211	γ = 120

Symmetry
Space Group	P 63

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		2006-05-23	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	2.5	30	99.3	0.081	0.081	97	8	17408	17286	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	2.5	2.59	99.7		0.608	0.608	4.2	7.4	1884

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	humane GITRL from C2 spacegroup	2.5	30	17408	17286	1067	95.75	0.22099	0.21747	0.21	0.2761	0.27	RANDOM	38.392

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]
0.08	0.04		0.08		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.106
r_dihedral_angle_3_deg	24.108
r_dihedral_angle_4_deg	23.208
r_dihedral_angle_1_deg	10.363
r_scangle_it	5.537
r_scbond_it	3.837
r_angle_refined_deg	2.964
r_mcangle_it	2.603
r_mcbond_it	1.655
r_nbtor_refined	0.348
r_symmetry_vdw_refined	0.334
r_nbd_refined	0.305
r_chiral_restr	0.234
r_xyhbond_nbd_refined	0.201
r_symmetry_hbond_refined	0.188
r_bond_refined_d	0.034
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3264
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing