1ZH2 | pdb_00001zh2

Crystal Structure Of The Calcium-Bound Receiver Domain Of Kdp Potassium Transport System Response Regulator KdpE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XHF	PDB ENTRY 1XHF (Ala Model)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	PEG 8000, Calcium Acetate, MES Buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.372	α = 90
b = 127.162	β = 90
c = 65.207	γ = 90

Symmetry
Space Group	C 2 2 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 4		2004-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	1.07179	NSLS	X4A

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	2	30	100	0.063	48	13.6	20179	20163		-3	12.3

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)
	2	2.07	99.9		0.159	24.2	10.2	1992

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1XHF (Ala Model)	2	30	20162	18100	2046	99.99	0.19831	0.19334	0.2	0.24184	0.24	RANDOM	25.051

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]
-1.03			1.04		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.585
r_scangle_it	3.099
r_mcangle_it	2.599
r_scbond_it	1.929
r_angle_refined_deg	1.556
r_mcbond_it	1.536
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.212
r_symmetry_hbond_refined	0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.585
r_scangle_it	3.099
r_mcangle_it	2.599
r_scbond_it	1.929
r_angle_refined_deg	1.556
r_mcbond_it	1.536
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.212
r_symmetry_hbond_refined	0.2
r_chiral_restr	0.118
r_metal_ion_refined	0.108
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1869
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	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.