2XCS

The 2.1A crystal structure of S. aureus Gyrase complex with GSK299423 and DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XCQPDB ENTRY 2XCQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.518% PEG 5000MME, 0.1 M BISTRIS PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.9257.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.318α = 90
b = 93.318β = 90
c = 412.812γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.13098.60.1211.4511316828.25
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2198.60.452.64.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2XCQ2.12011316829071000.183730.182950.21379RANDOM38.417
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]
-0.34-0.17-0.340.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.817
r_dihedral_angle_4_deg14.052
r_dihedral_angle_3_deg9.558
r_scangle_it3.576
r_dihedral_angle_1_deg2.563
r_scbond_it2.362
r_mcangle_it1.519
r_angle_refined_deg1.268
r_mcbond_it0.748
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.817
r_dihedral_angle_4_deg14.052
r_dihedral_angle_3_deg9.558
r_scangle_it3.576
r_dihedral_angle_1_deg2.563
r_scbond_it2.362
r_mcangle_it1.519
r_angle_refined_deg1.268
r_mcbond_it0.748
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.005
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_other
r_long_range_B_refined
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 Atoms10606
Nucleic Acid Atoms800
Solvent Atoms826
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing