8SDR

Crystal structure of PDC-3 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 DROP273100 mM Imidazole pH 7.0, 2-8% isopropyl alcohol (IPA), and 16-34% PEG 3350. Protein was in 10 mM HEPES pH 7.5, 150 mM NaCl and 5% glycerol
Crystal Properties
Matthews coefficientSolvent content
1.9737.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.828α = 90
b = 71.667β = 90
c = 106.729γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.97933NSLS-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
11.352899.70.1340.99814.812.876325
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)
11.351.3896.10.6260.8963

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 REPLACEMENTTHROUGHOUT1.352872326391999.690.13090.12920.1615RANDOM11.046
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]
-0.110.020.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.605
r_dihedral_angle_4_deg15.149
r_dihedral_angle_3_deg12.894
r_dihedral_angle_1_deg6.408
r_angle_refined_deg1.605
r_angle_other_deg1.493
r_rigid_bond_restr1.285
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.605
r_dihedral_angle_4_deg15.149
r_dihedral_angle_3_deg12.894
r_dihedral_angle_1_deg6.408
r_angle_refined_deg1.605
r_angle_other_deg1.493
r_rigid_bond_restr1.285
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2781
Nucleic Acid Atoms
Solvent Atoms593
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing