4DUH

Crystal structure of 24 kDa domain of E. coli DNA gyrase B in complex with small molecule inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KZNPDB entry 1KZN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.42930.1M MES, 22% PEG 3350, 0.2M NaNO3, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.236α = 90
b = 51.122β = 95.68
c = 79.13γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225Mirrors2011-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
11.578.7499.20.05113.87.3682646747811
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)
11.51.5399.60.4767.33350

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB entry 1KZN1.5209826467460342098.870.19320.19150.2255RANDOM26.9519
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]
-0.66-0.430.460.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.108
r_dihedral_angle_4_deg17.271
r_dihedral_angle_3_deg13.738
r_dihedral_angle_1_deg6.829
r_scangle_it6.372
r_scbond_it3.979
r_mcangle_it2.829
r_mcbond_it1.747
r_angle_refined_deg1.528
r_chiral_restr0.153
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.108
r_dihedral_angle_4_deg17.271
r_dihedral_angle_3_deg13.738
r_dihedral_angle_1_deg6.829
r_scangle_it6.372
r_scbond_it3.979
r_mcangle_it2.829
r_mcbond_it1.747
r_angle_refined_deg1.528
r_chiral_restr0.153
r_bond_refined_d0.018
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3008
Nucleic Acid Atoms
Solvent Atoms477
Heterogen Atoms52

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
PHASERphasing