3DGF | pdb_00003dgf

Structure of a histidine kinase-response regulator complex reveals insights into Two-component signaling and a novel cis-autophosphorylation mechanism

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		RR468 from the entry 2008-Jun-12.09.34.07.979392.Session.11388

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	294	28% PEG8000, 0.2M ammonium sulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.574	α = 90
b = 55.476	β = 90
c = 58.428	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	110	CCD	MAR CCD 165 mm	mirror	2005-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	1.008	ESRF	BM16

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	22.1	99.3	0.088	0.088	8.8	5.1	7951	40193		3	32.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	100		0.383	0.383	3.9	5.1	1143

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	RR468 from the entry 2008-Jun-12.09.34.07.979392.Session.11388	2	22.1	7328	40193	594	98.94	0.214	0.214	0.211	0.21	0.259	0.19	RANDOM	34.57

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]
-1.15			0.21		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.492
r_dihedral_angle_4_deg	25.873
r_dihedral_angle_3_deg	18.396
r_dihedral_angle_1_deg	9.744
r_scangle_it	5.187
r_scbond_it	3.208
r_mcangle_it	2.225
r_mcbond_it	1.91
r_angle_refined_deg	1.6
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.492
r_dihedral_angle_4_deg	25.873
r_dihedral_angle_3_deg	18.396
r_dihedral_angle_1_deg	9.744
r_scangle_it	5.187
r_scbond_it	3.208
r_mcangle_it	2.225
r_mcbond_it	1.91
r_angle_refined_deg	1.6
r_nbtor_refined	0.317
r_nbd_refined	0.275
r_symmetry_hbond_refined	0.249
r_xyhbond_nbd_refined	0.223
r_symmetry_vdw_refined	0.193
r_chiral_restr	0.126
r_bond_refined_d	0.02
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	952
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	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.