3BS1 | pdb_00003bs1

Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with a Novel Mode of Binding

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	40% PEG 400, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.938	α = 90
b = 47.938	β = 90
c = 100.112	γ = 90

Symmetry
Space Group	P 41

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		2006-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.9204	NSLS	X4A

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	1.6	17.3	98.1		3.8	29714	29714			18.4

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)
	1.6	1.66	97.3		0.155	5.7	3.8

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	SAD	THROUGHOUT	1.6	17.3	29714	27747	1485	98.35	0.1961	0.19659	0.19534	0.21	0.22066	0.23	RANDOM	19.945

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	37.564
r_dihedral_angle_4_deg	13.397
r_dihedral_angle_3_deg	11.461
r_dihedral_angle_1_deg	5.998
r_scangle_it	1.996
r_angle_refined_deg	1.381
r_scbond_it	1.364
r_mcangle_it	1.216
r_mcbond_it	0.768
r_xyhbond_nbd_refined	0.374

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.564
r_dihedral_angle_4_deg	13.397
r_dihedral_angle_3_deg	11.461
r_dihedral_angle_1_deg	5.998
r_scangle_it	1.996
r_angle_refined_deg	1.381
r_scbond_it	1.364
r_mcangle_it	1.216
r_mcbond_it	0.768
r_xyhbond_nbd_refined	0.374
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.187
r_symmetry_hbond_refined	0.155
r_chiral_restr	0.073
r_metal_ion_refined	0.023
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	872
Nucleic Acid Atoms	650
Solvent Atoms	223
Heterogen Atoms	2

Software

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

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.