8G2T

CRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH RELEBACTAM (IMINE HYDROLYSIS INTERMEDIATE)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OV5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293100 mM HEPES pH 8.0 and 0.8 M NaH2PO4, 0.8 M KH2PO4
Crystal Properties
Matthews coefficientSolvent content
2.1843.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.795α = 90
b = 66.227β = 90
c = 72.977γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-08-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.97935NSLS-II17-ID-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.2629.6399.90.06812113.166874
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.261.2998.40.6830.9313.512.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT2OV51.2627.7663495330999.870.135380.133720.16746RANDOM14.705
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]
-0.020.07-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.109
r_dihedral_angle_4_deg15.743
r_dihedral_angle_3_deg12.201
r_mcangle_it6.883
r_mcangle_other6.882
r_dihedral_angle_1_deg6.593
r_long_range_B_refined6.231
r_long_range_B_other6.012
r_rigid_bond_restr4.975
r_mcbond_other4.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.109
r_dihedral_angle_4_deg15.743
r_dihedral_angle_3_deg12.201
r_mcangle_it6.883
r_mcangle_other6.882
r_dihedral_angle_1_deg6.593
r_long_range_B_refined6.231
r_long_range_B_other6.012
r_rigid_bond_restr4.975
r_mcbond_other4.631
r_mcbond_it4.628
r_scangle_other3.089
r_scbond_other2.546
r_scbond_it2.544
r_angle_other_deg1.513
r_angle_refined_deg1.502
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1965
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms24

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing