3O02 | pdb_00003o02

The Crystal Structure of the Salmonella Type III Secretion System Tip Protein SipD in Complex with Chenodeoxycholate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	25% (w/v) PEG 3350, 100mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 202.216	α = 90
b = 52.37	β = 90.2
c = 57.316	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	CCD	ADSC QUANTUM 210r		2009-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-BM	1.0	APS	17-BM

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	1.9	37.96	97.9	0.053	27.9	3.7	46661	44253			24.26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.949	81.97

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	37.9	46661	44253	2354	97.97	0.19891	0.19651	0.2	0.24361	0.25	RANDOM	24.263

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.694
r_dihedral_angle_3_deg	15.184
r_dihedral_angle_4_deg	12.779
r_dihedral_angle_1_deg	4.685
r_scangle_it	3.902
r_scbond_it	2.639
r_mcangle_it	1.538
r_angle_refined_deg	1.442
r_mcbond_it	0.992
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.694
r_dihedral_angle_3_deg	15.184
r_dihedral_angle_4_deg	12.779
r_dihedral_angle_1_deg	4.685
r_scangle_it	3.902
r_scbond_it	2.639
r_mcangle_it	1.538
r_angle_refined_deg	1.442
r_mcbond_it	0.992
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.145
r_metal_ion_refined	0.131
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4227
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	29

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.