5NAI

mono-Zinc VIM-5 metallo-beta-lactamase in complex with (1-chloro-4-hydroxyisoquinoline-3-carbonyl)-D-tryptophan (Compound 1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A87 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.2 M Sodium fluoride, 0.1 M Bis-Tris propane, 20% (w/v) Polyethylene glycol 3350, pH=8.5
Crystal Properties
Matthews coefficientSolvent content
1.9135.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.553α = 90
b = 67.555β = 92.66
c = 40.093γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.0DiamondI04

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
11.15501000.0688.86.474624
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)
11.151.191000.3986

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5A871.153.891.3872606195099.90.1310.1310.14121.05
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1713
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms40

Software

Software
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction