Experiment: 3NEH

Crystal structure of the protein LMO2462 from Listeria monocytogenes complexed with ZN and phosphonate mimic of dipeptide L-Leu-D-Ala

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LU2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	25% PEG 3350, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.834	α = 90
b = 79.453	β = 90
c = 152.014	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	ADSC QUANTUM 4		2010-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97915	NSLS	X4A

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	1.642	39.727	93.95	0.094			75524	75524

Refinement

Statistics
Diffraction ID	Structure Solution 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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	3LU2	1.642	39.727	75524	75524	3802	93.95	0.1979	0.1979	0.1967	0.2193	0.2076

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]
-2.7282			5.7448		-3.0166

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.708
f_angle_d	1.073
f_chiral_restr	0.074
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4928
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	34

Software

Software
Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling