8BP2

2.8A STRUCTURE OF ZOLIFLODACIN WITH S.AUREUS DNA GYRASE AND DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CDM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.329390 mM bistris pH 6.3, 9% PEG 5000MME
Crystal Properties
Matthews coefficientSolvent content
3.2862.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.542α = 90
b = 94.542β = 90
c = 417.134γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 9M2022-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9999DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.78251000.9975.918.552704
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.782.830.318

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5CDM2.824.85451323253899.4050.1930.19080.231492.396
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]
2.231.1152.23-7.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.114
r_dihedral_angle_4_deg17.035
r_dihedral_angle_3_deg16.392
r_lrange_it12.356
r_dihedral_angle_1_deg5.768
r_scangle_it4.387
r_mcangle_it3.131
r_scbond_it2.739
r_mcbond_it1.817
r_angle_refined_deg1.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.114
r_dihedral_angle_4_deg17.035
r_dihedral_angle_3_deg16.392
r_lrange_it12.356
r_dihedral_angle_1_deg5.768
r_scangle_it4.387
r_mcangle_it3.131
r_scbond_it2.739
r_mcbond_it1.817
r_angle_refined_deg1.722
r_nbtor_refined0.32
r_symmetry_nbd_refined0.253
r_nbd_refined0.221
r_xyhbond_nbd_refined0.18
r_symmetry_xyhbond_nbd_refined0.167
r_chiral_restr0.114
r_bond_refined_d0.009
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10545
Nucleic Acid Atoms801
Solvent Atoms227
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing