8SK2

X-ray structure of the NDM-4 beta-lactamase from Klebsiella pneumonia, apo form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629318 - 26% (w/v) poly(ethylene glycol) 3350, 2% (v/v) dimethyl sulfoxide, and 100 mM MES (pH 6.0)
Crystal Properties
Matthews coefficientSolvent content
1.7228.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.927α = 90
b = 59.312β = 98.65
c = 41.815γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2022-01-18MSINGLE 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
11.35098.30.05116.15.246573
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)
11.31.496.40.3413.12.8

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 REPLACEMENTTHROUGHOUT1.333.9144388223598.330.179070.178040.19896RANDOM9.894
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_deg14.713
r_dihedral_angle_2_deg7.77
r_dihedral_angle_1_deg7.261
r_long_range_B_refined3.868
r_long_range_B_other3.606
r_scangle_other2.491
r_scbond_it1.786
r_scbond_other1.785
r_mcangle_other1.475
r_mcangle_it1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.713
r_dihedral_angle_2_deg7.77
r_dihedral_angle_1_deg7.261
r_long_range_B_refined3.868
r_long_range_B_other3.606
r_scangle_other2.491
r_scbond_it1.786
r_scbond_other1.785
r_mcangle_other1.475
r_mcangle_it1.47
r_angle_refined_deg1.432
r_mcbond_it1.011
r_mcbond_other1.006
r_angle_other_deg0.503
r_chiral_restr0.077
r_gen_planes_refined0.008
r_bond_refined_d0.007
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 Atoms1698
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing