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)
TypeSourceAccession CodeDetails
experimental modelPDB 1AB4PDB ENTRY 1AB4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298The 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 coefficientSolvent content
3.463.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.92α = 90
b = 137.85β = 90
c = 326.02γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platetwo cylindrical parabolic mirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.91694ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.670.0935.485197

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1AB42.6750085197821997.20.22350.2758RANDOM64.915
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]
-7.871-6.11313.983
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it2.224
c_mcangle_it2.075
c_scbond_it1.337
c_mcbond_it1.163
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13620
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
XSCALEdata scaling
CNSphasing