8SKP

X-ray structure of the NDM-4 beta-lactamase from Klebsiella pneumonia in complex with 1-hydroxypyridine-2(1H)-thione-6-carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8SK2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293Protein incubated with 10 mM 1-hydroxypyridine-2(1H)-thione-6-carboxylic acid. Precipitant: 18 - 26% (w/v) poly(ethylene glycol) 3350, 2% (v/v) dimethyl sulfoxide, and 100 mM MES (pH 6.0)
Crystal Properties
Matthews coefficientSolvent content
2.0539.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.138α = 90
b = 59.185β = 98.5
c = 42.266γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2022-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.5418

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
11.35092.70.04916.54.844587
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)
11.31.477.50.2862.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.332.9742417217092.680.203490.202430.22376RANDOM14.284
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
r_dihedral_angle_3_deg15.656
r_dihedral_angle_2_deg9.043
r_dihedral_angle_1_deg7.316
r_long_range_B_refined5.187
r_long_range_B_other5.186
r_scangle_other2.741
r_mcangle_other2.229
r_mcangle_it2.228
r_scbond_it1.926
r_scbond_other1.925
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.656
r_dihedral_angle_2_deg9.043
r_dihedral_angle_1_deg7.316
r_long_range_B_refined5.187
r_long_range_B_other5.186
r_scangle_other2.741
r_mcangle_other2.229
r_mcangle_it2.228
r_scbond_it1.926
r_scbond_other1.925
r_mcbond_it1.534
r_mcbond_other1.528
r_angle_refined_deg1.364
r_angle_other_deg0.469
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1706
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing