1Y9T

Crystal structure of a type III secretion system protein complexed with the lipid, 1-monohexanoyl-2-hydroxy-sn-glycero-3-phosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	(NH3)2SO4 LiSO4 NaCHOCH3, 1-monohexanoyl-2-hydroxy-sn-glycero-3-phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.036	α = 90
b = 49.721	β = 101.99
c = 29.52	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	MARRESEARCH	MIRRORS	2004-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.87	42.4	96.37	0.027	34	4.6	9460	9460			32.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.87	1.94	93.6		0.22	6.2	3.9	912

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1Y9L	1.87	42.4	9301	8964	496	96.37	0.20843	0.20843	0.20613	0.24907	EQUIVALENT RFREE REFLECTIONS TO PDB ENTRY 1Y9L (RANDOM)	33.85

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]
-0.35		-0.07	0.7		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.477
r_dihedral_angle_3_deg	15.501
r_dihedral_angle_4_deg	11.05
r_dihedral_angle_1_deg	6.918
r_scangle_it	3.603
r_scbond_it	2.268
r_mcangle_it	1.531
r_angle_refined_deg	1.473
r_mcbond_it	0.976
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.253
r_symmetry_hbond_refined	0.226
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.105
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_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	870
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling