5IDH

Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with 8-bromooctanoic acid

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	289	1.5 UL PROTEIN + 1.5 UL BUFFER (35% PEG3350, 0.1 M SODIUM CACODYLATE, 0.2 M SODIUM CHLORIDE, PH 5.75)

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.968	α = 90
b = 67.757	β = 115.73
c = 54.193	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	MARMOSAIC 300 mm CCD		2013-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

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	1.55	50	99.9	0.044	14.4	4.2		47386

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	1.55	1.58	100		0.398		4.1

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	5IBY	1.55	48	44806	2392	99.81	0.1802	0.1782	0.2167	RANDOM	24.408

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]
0.39		0.19	0.49		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.467
r_dihedral_angle_4_deg	15.02
r_dihedral_angle_3_deg	11.504
r_dihedral_angle_1_deg	6.279
r_mcangle_it	2.789
r_mcbond_it	2.187
r_mcbond_other	2.181
r_angle_refined_deg	1.204
r_angle_other_deg	0.722
r_chiral_restr	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.467
r_dihedral_angle_4_deg	15.02
r_dihedral_angle_3_deg	11.504
r_dihedral_angle_1_deg	6.279
r_mcangle_it	2.789
r_mcbond_it	2.187
r_mcbond_other	2.181
r_angle_refined_deg	1.204
r_angle_other_deg	0.722
r_chiral_restr	0.072
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2556
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	22

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 R01GM133198.