3SON

Crystal structure of a putativel NUDIX hydrolase (LMOf2365_2679) from Listeria monocytogenes str. 4b F2365 at 1.70 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	10.0% 2-propanol, 0.2M Ca(OAc)2, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.88	α = 90
b = 57.88	β = 90
c = 94.49	γ = 90

Symmetry
Space Group	P 43

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 325 mm CCD	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)	2007-07-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97937,0.97908	SSRL	BL11-1

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	1.7	27.671	99	0.042	13.88			34048		-3	26.769

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	1.7	1.75	99.8		0.426	3.1	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.71	27.671	33655	1742	99.59	0.1651	0.1634	0.196	RANDOM + TWIN LAW	31.6546

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]
14.38			14.38		-28.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.297
r_dihedral_angle_3_deg	11.753
r_dihedral_angle_4_deg	11.448
r_dihedral_angle_1_deg	6.196
r_angle_refined_deg	1.565
r_angle_other_deg	0.901
r_chiral_restr	0.103
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.297
r_dihedral_angle_3_deg	11.753
r_dihedral_angle_4_deg	11.448
r_dihedral_angle_1_deg	6.196
r_angle_refined_deg	1.565
r_angle_other_deg	0.901
r_chiral_restr	0.103
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2341
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	2

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	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.