8RTZ

The structure of E. coli penicillin binding protein 3 (PBP3) in complex with a bicyclic peptide inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I1IPiperacillin was removed

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92770.1M Tris pH 9.0 and 20% (w/v) PEG 6K supplemented with an additive, 30% (w/v) dextran sulphate sodium salt, Mr 5K
Crystal Properties
Matthews coefficientSolvent content
2.1142.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.89α = 90
b = 152.181β = 90
c = 43.675γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2020-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5245.0499.6123.812.250525
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.521.55930.7497.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5245.0450510252599.580.1840.18190.215724.42
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]
3.04-1.971-1.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.319
r_dihedral_angle_other_3_deg17.939
r_dihedral_angle_4_deg14.285
r_dihedral_angle_3_deg13.146
r_dihedral_angle_1_deg6.815
r_lrange_it6.377
r_lrange_other6.376
r_scangle_it4.376
r_scangle_other4.375
r_mcangle_it3.241
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.319
r_dihedral_angle_other_3_deg17.939
r_dihedral_angle_4_deg14.285
r_dihedral_angle_3_deg13.146
r_dihedral_angle_1_deg6.815
r_lrange_it6.377
r_lrange_other6.376
r_scangle_it4.376
r_scangle_other4.375
r_mcangle_it3.241
r_mcangle_other3.241
r_scbond_it2.848
r_scbond_other2.847
r_mcbond_it2.174
r_mcbond_other2.169
r_angle_refined_deg1.738
r_angle_other_deg1.438
r_symmetry_nbd_refined0.348
r_nbd_other0.262
r_nbd_refined0.228
r_xyhbond_nbd_refined0.188
r_symmetry_nbd_other0.187
r_nbtor_refined0.17
r_symmetry_xyhbond_nbd_refined0.164
r_chiral_restr0.09
r_symmetry_nbtor_other0.084
r_symmetry_xyhbond_nbd_other0.075
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2525
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing