3R07

Structural analysis of an archaeal lipoylation system. A bi-partite lipoate protein ligase and its E2 lipoyl domain from Thermoplasma acidophilum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ARS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6	291	40% v/v MPD, 0.1M sodium acetate, 0.02M calcium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.57	α = 90
b = 118.57	β = 90
c = 72.92	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	ADSC QUANTUM 315r	VORTEX FLUORESCENCE DETECTOR	2009-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	38.81

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	2ARS	2.7	38.81	15063	789	100	0.2	0.198	0.254	RANDOM	51.56

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]
-0.03	-0.01		-0.03		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.478
r_dihedral_angle_3_deg	19.139
r_dihedral_angle_4_deg	17.592
r_dihedral_angle_1_deg	6.489
r_scangle_it	3.872
r_scbond_it	2.427
r_mcangle_it	1.742
r_angle_refined_deg	1.547
r_mcbond_it	1.012
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.22
r_symmetry_hbond_refined	0.196
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2761
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	24

Software

Software
Software Name	Purpose
ADSC	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling