3PN1

Novel Bacterial NAD+-dependent DNA Ligase Inhibitors with Broad Spectrum Potency and Antibacterial Efficacy In Vivo

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		16% (w/v) polyethylene glycol (PEG) 3500, 350mM sodium potassium tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.71	66.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.806	α = 90
b = 137.806	β = 90
c = 56.023	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	RIGAKU SATURN 944			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ DW

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	25.95	99				36612

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	25.95	36612	1827	98.95	0.2029	0.2014	0.2312	RANDOM	27.4439

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.133
r_dihedral_angle_4_deg	20.798
r_dihedral_angle_3_deg	15.171
r_dihedral_angle_1_deg	6.766
r_scangle_it	5.214
r_scbond_it	3.386
r_mcangle_it	2.175
r_angle_refined_deg	2.052
r_mcbond_it	1.269
r_chiral_restr	0.143

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.133
r_dihedral_angle_4_deg	20.798
r_dihedral_angle_3_deg	15.171
r_dihedral_angle_1_deg	6.766
r_scangle_it	5.214
r_scbond_it	3.386
r_mcangle_it	2.175
r_angle_refined_deg	2.052
r_mcbond_it	1.269
r_chiral_restr	0.143
r_bond_refined_d	0.026
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2515
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
SCALA	data scaling
AMoRE	phasing

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.