2PKX | pdb_00002pkx

E.coli response regulator PhoP receiver domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PL1	activated ecoli PhoP receiver domain structure without alpha helix 4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	298	precipitant: Sodium thiocyanate, Peg3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.645	α = 90
b = 102.645	β = 90
c = 62.641	γ = 120

Symmetry
Space Group	P 65

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	Spherical mirrors	2004-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	1.07217	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	2.45	30	98.84	0.113	13.51	4.96	13947	13785		-3	57.9

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)
	2.45	2.54	99.1		0.61	1.36	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	activated ecoli PhoP receiver domain structure without alpha helix 4	2.54	30	-3	11296	11245	1239	99.54	0.21029	0.20555	0.22	0.25284	0.26	RANDOM	44.743

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]
0.59	0.3		0.59		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.311
r_dihedral_angle_4_deg	18.279
r_dihedral_angle_3_deg	17.414
r_dihedral_angle_1_deg	5.841
r_scangle_it	3.588
r_scbond_it	2.274
r_angle_refined_deg	1.826
r_mcangle_it	1.448
r_mcbond_it	0.995
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.265
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.111
r_bond_refined_d	0.019
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1885
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing