3D6W

LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.4 M magnesium chloride, 0.1 M HEPES buffer. Full length protein consisting of 214 original residues was used for crystallization. The obtained crystals contain only C-terminal domain of the protein, probably, due to proteolysis of the protein in crystallization conditions. , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.784	α = 90
b = 88.784	β = 90
c = 74.425	γ = 90

Symmetry
Space Group	P 42 2 2

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 315		2008-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

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	2.4	48	100	0.073	13.6	27.8	12166	12166			65.6

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	2.44	100		0.913	4.4	26.7	583

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.4	48	12141	12141	581	99.93	0.184	0.184	0.182	0.209	RANDOM	50.238

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]
0.43			0.43		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.831
r_dihedral_angle_3_deg	20.146
r_dihedral_angle_4_deg	15.267
r_dihedral_angle_1_deg	7.001
r_scangle_it	3.263
r_scbond_it	2.222
r_mcangle_it	1.701
r_angle_refined_deg	1.664
r_mcbond_it	1.348
r_angle_other_deg	0.984
r_nbd_refined	0.213
r_nbd_other	0.207
r_symmetry_vdw_other	0.207
r_symmetry_hbond_refined	0.194
r_nbtor_refined	0.19
r_mcbond_other	0.189
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.099
r_nbtor_other	0.095
r_symmetry_vdw_refined	0.08
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1778
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing