6QTK

2.31A structure of gepotidacin with S.aureus DNA gyrase and doubly nicked DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XCS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH29311% PEG 5000MME, BisTris pH 6.2
Crystal Properties
Matthews coefficientSolvent content
3.0159.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.73α = 90
b = 92.73β = 90
c = 408.775γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.314099.719.25.585905
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.312.35

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2XCS2.3139.9982431342699.740.164210.162570.20347RANDOM35.747
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]
-0.1-0.05-0.10.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.731
r_dihedral_angle_4_deg17.28
r_dihedral_angle_3_deg13.222
r_long_range_B_refined7.833
r_dihedral_angle_1_deg5.782
r_scbond_it3.997
r_mcangle_it3.634
r_mcbond_it2.61
r_angle_refined_deg1.448
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.731
r_dihedral_angle_4_deg17.28
r_dihedral_angle_3_deg13.222
r_long_range_B_refined7.833
r_dihedral_angle_1_deg5.782
r_scbond_it3.997
r_mcangle_it3.634
r_mcbond_it2.61
r_angle_refined_deg1.448
r_chiral_restr0.096
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10625
Nucleic Acid Atoms807
Solvent Atoms823
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing