3CNY

Crystal structure of a putative inositol catabolism protein iole (iole, lp_3607) from lactobacillus plantarum wcfs1 at 1.85 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	NANODROP, 0.2M (NH4)2H Citrate, 20.0% PEG 3350, No Buffer pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.235	α = 90
b = 51.553	β = 90
c = 246.908	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 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97908	SSRL	BL9-2

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	1.8	29.273	99.4	0.089	12			57200		-3	20.373

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)
	1.8	1.86	95.9		0.74	2.3

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	SAD	THROUGHOUT	1.85	29.273	57116	2891	99.7	0.167	0.165	0.21	RANDOM	16.493

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			-0.55		-1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.596
r_dihedral_angle_3_deg	12.718
r_dihedral_angle_4_deg	10.57
r_dihedral_angle_1_deg	5.784
r_scangle_it	5.323
r_scbond_it	4.319
r_mcangle_it	2.46
r_mcbond_it	1.888
r_angle_refined_deg	1.398
r_angle_other_deg	0.952
r_mcbond_other	0.696
r_symmetry_vdw_other	0.227
r_nbd_refined	0.208
r_nbd_other	0.193
r_nbtor_refined	0.182
r_symmetry_hbond_refined	0.174
r_xyhbond_nbd_refined	0.154
r_symmetry_vdw_refined	0.123
r_chiral_restr	0.094
r_nbtor_other	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4747
Nucleic Acid Atoms
Solvent Atoms	749
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing
SHELXD	phasing