4PRV

E. coli GyrB 43-kDa N-terminal fragment in complex with ADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293.1510%(w/v) PEG20000, 20%(v/v) PEGMME550, 0.02M each carboxylic acid, 0.1M bicine/Trizma base pH 8.5, vapor diffusion, sitting drop, temperature 293.15K
Crystal Properties
Matthew coefficientSolvent content
3.0559.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.25α = 90
b = 142.52β = 90
c = 79.09γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0000SLSX06DA

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
1275.0388.20.06822.153005330053-332.303
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1295.80.5830.6443.32

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT1EI1275.03-33005230052201188.220.21020.20670.2587RANDOM28.952
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]
-1.421.97-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.496
r_dihedral_angle_4_deg19.323
r_dihedral_angle_3_deg15.165
r_dihedral_angle_1_deg6.29
r_angle_refined_deg1.883
r_angle_other_deg0.915
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.496
r_dihedral_angle_4_deg19.323
r_dihedral_angle_3_deg15.165
r_dihedral_angle_1_deg6.29
r_angle_refined_deg1.883
r_angle_other_deg0.915
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2828
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms28

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction