3A0T | pdb_00003a0t

Catalytic domain of histidine kinase ThkA (TM1359) in complex with ADP and Mg ion (trigonal)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		nucleotide free structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	5% isopropanol, 2.0M ammonium sulphate, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.95	68.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.943	α = 90
b = 72.943	β = 90
c = 91.258	γ = 120

Symmetry
Space Group	P 32 2 1

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		2006-09-28	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	1.91	50	100	0.049	51.6	12.1		22342		-3	24.8

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	1.91	1.98	100		0.432	6	11.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	nucleotide free structure	1.91	20	22252	1133	99.99	0.186	0.185	0.18	0.213	0.21	RANDOM	26.301

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]
0.15	0.08		0.15		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.697
r_dihedral_angle_3_deg	17.443
r_dihedral_angle_4_deg	15.472
r_scangle_it	9.267
r_dihedral_angle_1_deg	6.769
r_scbond_it	6.164
r_mcangle_it	4.258
r_mcbond_it	3.306
r_angle_refined_deg	1.93
r_nbtor_refined	0.339

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.697
r_dihedral_angle_3_deg	17.443
r_dihedral_angle_4_deg	15.472
r_scangle_it	9.267
r_dihedral_angle_1_deg	6.769
r_scbond_it	6.164
r_mcangle_it	4.258
r_mcbond_it	3.306
r_angle_refined_deg	1.93
r_nbtor_refined	0.339
r_nbd_refined	0.328
r_symmetry_vdw_refined	0.239
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.115
r_chiral_restr	0.106
r_gen_planes_refined	0.013
r_bond_refined_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1246
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	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.