7TC1

Crystal structure of D179N KPC-2 beta-lactamase in complex with vaborbactam


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42980.1 M Sodium citrate HCl pH 4, 0.8 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.1943.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.209α = 90
b = 66.021β = 90
c = 72.95γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2020-08-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.97935NSLS-II17-ID-1

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
11.1627.7698.80.064120.212.683367
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)
11.161.284.20.620.882.68.9

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 REPLACEMENTTHROUGHOUT2OV51.1627.7680550417198.560.12890.12740.1576RANDOM12.372
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]
-0.010.03-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.478
r_dihedral_angle_4_deg17.371
r_dihedral_angle_3_deg11.358
r_dihedral_angle_1_deg6.47
r_rigid_bond_restr4.315
r_angle_refined_deg2.002
r_angle_other_deg1.7
r_chiral_restr0.129
r_bond_refined_d0.017
r_gen_planes_refined0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.478
r_dihedral_angle_4_deg17.371
r_dihedral_angle_3_deg11.358
r_dihedral_angle_1_deg6.47
r_rigid_bond_restr4.315
r_angle_refined_deg2.002
r_angle_other_deg1.7
r_chiral_restr0.129
r_bond_refined_d0.017
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1977
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms30

Software

Software
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing