8SDS

Crystal structure of PDC-3 Y221H beta-lactamase in complex with the boronic acid inhibitor LP-06


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3S22 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7273100 mM Imidazole pH 7.0, 2-8% isopropyl alcohol (IPA), and 16-34% PEG 3350. The protein was in 10 mM HEPES pH 7.5, 150 mM NaCl and 5% glycerol
Crystal Properties
Matthews coefficientSolvent content
1.9737.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.133α = 90
b = 71.498β = 90
c = 105.932γ = 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
11.6328.0499.80.0970.99921.113.143613
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)
11.631.6797.80.8060.8973.4

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 REPLACEMENTTHROUGHOUT3S221.6328.0441300224699.790.15670.15490.1892RANDOM17.479
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.528
r_dihedral_angle_3_deg13.889
r_dihedral_angle_4_deg13.507
r_dihedral_angle_1_deg6.698
r_angle_refined_deg1.679
r_angle_other_deg1.415
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.528
r_dihedral_angle_3_deg13.889
r_dihedral_angle_4_deg13.507
r_dihedral_angle_1_deg6.698
r_angle_refined_deg1.679
r_angle_other_deg1.415
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2786
Nucleic Acid Atoms
Solvent Atoms508
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing