3A0Z

Catalytic domain of histidine kinase ThkA (TM1359) (nucleotide free form 4: isopropanol, orthorombic)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A0W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.6	293	20% isopropanol, 0.1M sodium citrate, 20% PEG4000, pH 5.6, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.31	α = 90
b = 61.094	β = 90
c = 89.952	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 210		2007-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	1.0	SPring-8	BL44B2

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	1.75	50	96	0.044	29.5	5		31968		-3	19.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.75	1.81	86.3		0.245	2.7	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	3A0W	1.75	30.77	31940	1621	95.99	0.198	0.195	0.241	RANDOM	20.355

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]
0.03			-0.59		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.04
r_dihedral_angle_4_deg	15.521
r_dihedral_angle_3_deg	14.525
r_dihedral_angle_1_deg	6.783
r_scangle_it	3.545
r_scbond_it	2.419
r_mcangle_it	1.574
r_angle_refined_deg	1.417
r_mcbond_it	0.99
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.04
r_dihedral_angle_4_deg	15.521
r_dihedral_angle_3_deg	14.525
r_dihedral_angle_1_deg	6.783
r_scangle_it	3.545
r_scbond_it	2.419
r_mcangle_it	1.574
r_angle_refined_deg	1.417
r_mcbond_it	0.99
r_nbtor_refined	0.312
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.172
r_symmetry_vdw_refined	0.153
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.099
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2538
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
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.