3U3P | pdb_00003u3p

The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.2M ammonium acetate, 0.1M sodium citrate tribasic dehydrate (pH5.0-6.0), 25-30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.857	α = 90
b = 77.857	β = 90
c = 186.381	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2011-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.9794	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.09	38.11	99.9				20449	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.09	38.11	19507	19478	1053	99.85	0.22746	0.22527	0.2222	0.27054	0.2653	RANDOM	35.296

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]
0.06	0.03		0.06		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.393
r_dihedral_angle_3_deg	19.585
r_dihedral_angle_4_deg	18.459
r_dihedral_angle_1_deg	7.873
r_angle_refined_deg	2.417
r_chiral_restr	0.18
r_bond_refined_d	0.023
r_gen_planes_refined	0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1229
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms

Software

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