4EHY | pdb_00004ehy

Crystal structure of LpxK from Aquifex aeolicus in complex with ADP/Mg2+ at 2.2 angstrom resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EHX	PDB ENTRY 4EHX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop, vapor diffusion	7.5	293	The reservoir solution contained 60% MPD and 0.1 M Hepes pH 7.5. The drop contained 20% seed stock, ~1 mg/ml protein, 48% MPD, 80 mM Hepes pH 7.5, 4 mM Hepes pH 8.0, 130 mM NaCl, 3.4% glycerol, ~0.06% DDM, 1.8 mM ATP, 1.8 mM MgCl2, sutting drop, vapor diffusion, temperature 293K, sitting drop, vapor diffusion

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.11	α = 90
b = 75.61	β = 90
c = 104.2	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	MARMOSAIC 225 mm CCD		2011-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.00	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.199	50	98	0.049	13.6	4.7	26821	26285	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.199	2.24	86.9		0.434		3.6	1151

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 4EHX	2.199	28.401	0.08	26285	24602	1999	91.73	0.1808	0.1779	0.2	0.2132	0.24	65.3908

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]
-0.2843			11.4845		-11.2002

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.299
f_angle_d	1.157
f_chiral_restr	0.073
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2520
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	47

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.