3L6H

Crystal structure of lactococcal OpuAC in its closed-liganded conformation complexed with glycine betaine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.2 M NaCl, 0.1 M Na-Hepes, pH 7.0, 20% PEG 6000, 1 mM glycine betaine, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.706	α = 90
b = 111.706	β = 90
c = 151.728	γ = 120

Symmetry
Space Group	H 3 2

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		2009-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.872	ESRF	ID23-2

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	2.2	46	97.4	0.114	10.71			16390		2	34.2

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)
	2.2	2.33	96.1		0.666	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB code 3L6G	2.3	40.78	16379	15560	819	100	0.19843	0.1972	0.22137	RANDOM	19.832

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]
-1.05	-0.53		-1.05		1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.819
r_dihedral_angle_3_deg	11.858
r_dihedral_angle_4_deg	9.882
r_dihedral_angle_1_deg	4.907
r_scangle_it	1.165
r_angle_refined_deg	0.898
r_angle_other_deg	0.778
r_scbond_it	0.7
r_mcangle_it	0.438
r_mcbond_it	0.22
r_chiral_restr	0.052
r_mcbond_other	0.032
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1995
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	10

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction