3M7O

Crystal structure of mouse MD-1 in complex with phosphatidylcholine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	22% (w/v) PEG-8000, 0.2 M Ammonium sulfate and MES pH 6.5,supplemented with 1/10 volume of 20% (w/v) benzamidine hydrochloride as a crystallization additive, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.299	α = 90
b = 90.299	β = 90
c = 86.714	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 270		2009-12-23	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210r			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A		Photon Factory	AR-NE3A
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A		Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.65	30	98.4	0.065				82260

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.65	1.68	86.9		0.566	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	SIRAS	THROUGHOUT	1.65	29.96	3	67139	3551	98.13	0.19624	0.1946	0.22659	RANDOM	38.359

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.484
r_dihedral_angle_4_deg	16.255
r_dihedral_angle_3_deg	13.639
r_scangle_it	7.089
r_dihedral_angle_1_deg	6.546
r_scbond_it	4.481
r_mcangle_it	3.372
r_mcbond_it	2.015
r_angle_refined_deg	1.405
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4135
Nucleic Acid Atoms
Solvent Atoms	444
Heterogen Atoms	364

Software

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