6BNF

Crystal structure of the intrinsic colistin resistance enzyme ICR(Mc) from Moraxella catarrhalis, catalytic domain, mono-zinc complex


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62980.1 M sodium acetate pH 4.6, 1.2 M ammonium sulfate, soaking 2.5 mM zinc chloride for 30 minutes. Cryoprotectant 8% glycerol, 8% ethylene glycol, 8% sucrose.
Crystal Properties
Matthews coefficientSolvent content
3.5865.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.272α = 90
b = 148.272β = 90
c = 148.272γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2016-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.27424APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.33104.841000.1610.02512476.524451
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.332.391003.9410.6720.841266.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6BNE2.3360.5321.3342891216395.280.21050.20850.2482RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.095
f_angle_d1.274
f_chiral_restr0.038
f_bond_d0.006
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2602
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms53

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building