1TJY | pdb_00001tjy

Crystal Structure of Salmonella typhimurium AI-2 receptor LsrB in complex with R-THMF

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	PEG 4000, sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.824	α = 90
b = 76.623	β = 90
c = 109.581	γ = 90

Symmetry
Space Group	P 21 21 21

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 4		2002-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

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	1.3	63.25	97	0.082	9.7			77033

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	1.3	1.334	87

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 (All)	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	1.3	63.25	76855	72992	3863	97.03	0.1578	0.15643	0.15563	0.17	0.17156	0.18	RANDOM	8.753

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]
-0.07			0.27		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.792
r_scangle_it	2.581
r_scbond_it	1.573
r_sphericity_free	1.325
r_angle_refined_deg	1.257
r_mcangle_it	1.068
r_sphericity_bonded	1.007
r_angle_other_deg	0.976
r_rigid_bond_restr	0.756
r_mcbond_it	0.604
r_symmetry_vdw_other	0.248
r_nbd_other	0.234
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.11
r_xyhbond_nbd_refined	0.103
r_chiral_restr	0.102
r_symmetry_vdw_refined	0.097
r_nbtor_other	0.084
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2412
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms	10

Software

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