3A0W | pdb_00003a0w

Catalytic domain of histidine kinase ThkA (TM1359) for MAD phasing (nucleotide free form 2, orthorombic)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	40% MPD, 0.1M sodium cacodylate, 5% PEG8000, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.092	α = 90
b = 61.148	β = 90
c = 90.287	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	RIGAKU JUPITER 210		2006-05-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0072, 1.0090, 0.9900	SPring-8	BL26B1

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	1.69	20	97.5	0.069	25.4	4		36504		-3	21.8

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)
	1.69	1.75	93		0.305	4.7	3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.69	20	36456	1832	97.45	0.214	0.213	0.21	0.24	0.24	RANDOM	23.063

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]
0.4			-0.87		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.293
r_dihedral_angle_4_deg	14.65
r_dihedral_angle_3_deg	14.146
r_dihedral_angle_1_deg	5.698
r_scangle_it	4.035
r_scbond_it	2.698
r_mcangle_it	1.849
r_angle_refined_deg	1.474
r_mcbond_it	1.172
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.293
r_dihedral_angle_4_deg	14.65
r_dihedral_angle_3_deg	14.146
r_dihedral_angle_1_deg	5.698
r_scangle_it	4.035
r_scbond_it	2.698
r_mcangle_it	1.849
r_angle_refined_deg	1.474
r_mcbond_it	1.172
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2499
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SPACE	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.