4XYQ

Structure of AgrA LytTR domain in complex with promoters

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	0.1M Bis-Tris pH 6.0, 40% PEG 400.

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.77	α = 90
b = 47.77	β = 90
c = 100.25	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	IMAGE PLATE	MAR scanner 300 mm plate		2012-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-002	1.54179

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	2.38	50.12	99.7	0.081	9.6	4.2		8820

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	2.4	2.49	100		0.461	2.9	4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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		THROUGHOUT	2.4	47.77	8347	437	99.6	0.2026	0.20084	0.23752	RANDOM	43.988

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]
1.8			1.8		-3.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.947
r_dihedral_angle_4_deg	16.831
r_dihedral_angle_3_deg	14.175
r_long_range_B_refined	9.083
r_long_range_B_other	9.083
r_scangle_other	6.691
r_dihedral_angle_1_deg	6.327
r_mcangle_it	4.63
r_mcangle_other	4.629
r_scbond_it	4.485
r_scbond_other	4.485
r_mcbond_it	3.115
r_mcbond_other	3.092
r_angle_refined_deg	1.537
r_angle_other_deg	1.306
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	865
Nucleic Acid Atoms	650
Solvent Atoms	22
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data reduction
SCALA	data scaling
PHASER	phasing