2NOV

Breakage-reunion domain of S.pneumoniae topo IV: crystal structure of a gram-positive quinolone target

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AB4	PDB ENTRY 1AB4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	The purified ParC55 protein was dialyzed against 20 mM Tris-HCl, pH 7.0, 200 mM NaCl, 10% glycerol, 1 mM beta-mercaptoethanol, 0.05% NaN3 then concentrated to 3-4 mg/ml. Hanging drops were formed by mixing equal volumes of protein and crystallization solutions (100 mM Tris-HCl, pH 5.5, 200 mM NaCl, 1 mM beta-mercaptoethanol, 0.05% NaN3 and 10% of 1:1 ethanol-isopropanol as precipitant). , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.92	α = 90
b = 137.85	β = 90
c = 326.02	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	two cylindrical parabolic mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.91694	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.67			0.093		5.4		85197

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1AB4	2.67	500	85197	8219	97.2	0.2235	0.2758	RANDOM	64.915

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]
-7.871			-6.113		13.983

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.224
c_mcangle_it	2.075
c_scbond_it	1.337
c_mcbond_it	1.163

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13620
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
CNS	phasing

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.