5IBY

Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with lipoic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VQZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.25	289	1.5 UL PROTEIN + 1.5 UL BUFFER (25% PEG3350, 0.1 M SODIUM CACODYLATE, 0.2 M SODIUM CHLORIDE, PH 5.25)

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.977	α = 90
b = 68.561	β = 116.13
c = 54.154	γ = 90

Symmetry
Space Group	P 1 21 1

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 210r		2014-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979054	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.85	50	99.5	0.036	0.04	0.018	19.8	4.9		28555

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	99.2		0.161	0.186	0.091	0.972		4	1411

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	1VQZ	1.85	21.5	27075	1443	99.4	0.1664	0.1641	0.2103	RANDOM	26.679

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]
-0.23		-0.25	2.17		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.99
r_dihedral_angle_4_deg	13.472
r_dihedral_angle_3_deg	12.509
r_dihedral_angle_1_deg	5.929
r_mcangle_it	2.065
r_mcbond_it	1.409
r_mcbond_other	1.403
r_angle_refined_deg	1.113
r_angle_other_deg	0.695
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.99
r_dihedral_angle_4_deg	13.472
r_dihedral_angle_3_deg	12.509
r_dihedral_angle_1_deg	5.929
r_mcangle_it	2.065
r_mcbond_it	1.409
r_mcbond_other	1.403
r_angle_refined_deg	1.113
r_angle_other_deg	0.695
r_chiral_restr	0.069
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2599
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction

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.