3NUH

A domain insertion in E. coli GyrB adopts a novel fold that plays a critical role in gyrase function


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AB4The structure was solved as a combination of MR and SAD method. The starting model used corresponds to PDB ID 1AB4.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop829190 mM imidazole pH 8.0, 11% isopropanol, 18 mM magnesium chloride, 10 mM spermidine, 3% pentaerythritol ethoxylate 15/4, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5652.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.062α = 90
b = 147.493β = 90
c = 138.87γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC Q315r2008-07-22SAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97920APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
13.135.699.60.10352032056.37
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.13.299.60.3873.84.6

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMR-SADThe structure was solved as a combination of MR and SAD method. The starting model used corresponds to PDB ID 1AB4.3.10335.61.938496377899.260.2380.2340.28282.602
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]
41.129-21.17-19.959
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.64
f_angle_d0.618
f_chiral_restr0.042
f_bond_d0.003
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6666
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms2

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction