5ICH

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.25	289	1.5 UL PROTEIN + 1.5 UL BUFFER (27% PEG3350, 0.1 M SODIUM CACODYLATE, 0.2 M SODIUM CHLORIDE, PH 5.25)

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.917	α = 90
b = 69.383	β = 92.3
c = 97.664	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	0.97905	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	99.8	0.037	0.041	0.018	23.7	4.9		58160

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	1.92	100		0.126	0.145	0.07	0.984		4.1	5822

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	1.85	21.5	55147	2935	99.79	0.1712	0.1694	0.2052	RANDOM	23.297

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]
-0.36		0.03	1.1		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.719
r_dihedral_angle_4_deg	16.051
r_dihedral_angle_3_deg	12.019
r_dihedral_angle_1_deg	6.057
r_mcangle_it	1.662
r_angle_refined_deg	1.186
r_mcbond_it	1.029
r_mcbond_other	1.029
r_angle_other_deg	0.722
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.719
r_dihedral_angle_4_deg	16.051
r_dihedral_angle_3_deg	12.019
r_dihedral_angle_1_deg	6.057
r_mcangle_it	1.662
r_angle_refined_deg	1.186
r_mcbond_it	1.029
r_mcbond_other	1.029
r_angle_other_deg	0.722
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5124
Nucleic Acid Atoms
Solvent Atoms	548
Heterogen Atoms	66

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 National Science Foundation (DBI-1832184), 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.