6F96

Crystal Structure of E. coli GyraseB 24kDa in complex with 6-[(ethylcarbamoyl)amino]-4-[(4-methoxyphenyl)amino]-N-(pyridin-3-yl)pyridine-3-carboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6F86 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529325-30% PEG 400 and 100 mM Hepes pH 6.5
Crystal Properties
Matthews coefficientSolvent content
359.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.2α = 90
b = 100.2β = 90
c = 50.27γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.550.271000.1860.1970.0630.99710.69.810325
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.571001.6911.7850.5670.5289.8

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6F862.550.27981249899.970.20880.20740.2383RANDOM47.287
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]
0.290.140.29-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.45
r_dihedral_angle_4_deg19.992
r_dihedral_angle_3_deg15.433
r_dihedral_angle_1_deg5.678
r_angle_refined_deg1.375
r_angle_other_deg0.966
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.45
r_dihedral_angle_4_deg19.992
r_dihedral_angle_3_deg15.433
r_dihedral_angle_1_deg5.678
r_angle_refined_deg1.375
r_angle_other_deg0.966
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1447
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms30

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction