2XCQ

The 2.98A crystal structure of the catalytic core (B'A' region) of Staphylococcus aureus DNA Gyrase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XCOPDB ENTRY 2XCO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
112.75% PEG 3350, 85MM MGFORMATE, 15% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
3.3863.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.118α = 90
b = 90.118β = 90
c = 416.14γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.981496.70.0713.32.81943499
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)
12.983.1499.90.471.92.8

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 2XCO2.9813.9919434107696.10.209140.205060.28637RANDOM19.425
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]
0.260.130.26-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.471
r_scangle_it5.334
r_scbond_it3.714
r_angle_refined_deg1.612
r_mcangle_it1.553
r_mcbond_it0.385
r_symmetry_hbond_refined0.258
r_nbd_refined0.257
r_symmetry_vdw_refined0.25
r_xyhbond_nbd_refined0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.471
r_scangle_it5.334
r_scbond_it3.714
r_angle_refined_deg1.612
r_mcangle_it1.553
r_mcbond_it0.385
r_symmetry_hbond_refined0.258
r_nbd_refined0.257
r_symmetry_vdw_refined0.25
r_xyhbond_nbd_refined0.167
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms5152
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing