3RAE

Quinolone(Levofloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K9F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION6.530450mM sodium cacodylate, 7% isopropanol, pH 6.5, LIQUID DIFFUSION, temperature 304K
Crystal Properties
Matthews coefficientSolvent content
4.1170.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.831α = 90
b = 157.831β = 90
c = 211.147γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.65099.10.0850.08513.7894.59401093164-371.22
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6995.30.840.841.23.58838

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3K9F2.941.8321.346747167471683899.450.18990.18570.2264Random
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]
6.80016.8001-13.6002
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.839
f_angle_d1.221
f_chiral_restr0.077
f_bond_d0.008
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10338
Nucleic Acid Atoms730
Solvent Atoms54
Heterogen Atoms58

Software

Software
Software NamePurpose
GDEdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling