6R42

Structure of R504C mutant of Pseudomonas aeruginosa Penicillin-Binding Protein 3 (PBP3) in complex with piperacillin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OC2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29325% (w/v) polyethylene glycol 3 350, 0.1 M Bis-Tris propane pH 7.8 and 1% (w/v) protamine sulphate
Crystal Properties
Matthews coefficientSolvent content
2.1542.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.44α = 90
b = 82.64β = 90
c = 88.76γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.98DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7254.2310013.811.554141
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)
11.721.750.5

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 REPLACEMENTTHROUGHOUT3OC21.7254.251309276199.880.210610.208460.25055RANDOM33.939
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]
2.95-0.93-2.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.086
r_dihedral_angle_4_deg17.131
r_dihedral_angle_3_deg15.608
r_long_range_B_refined7.339
r_long_range_B_other7.336
r_dihedral_angle_1_deg7.087
r_scangle_other5.594
r_mcangle_it4.18
r_mcangle_other4.18
r_scbond_it3.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.086
r_dihedral_angle_4_deg17.131
r_dihedral_angle_3_deg15.608
r_long_range_B_refined7.339
r_long_range_B_other7.336
r_dihedral_angle_1_deg7.087
r_scangle_other5.594
r_mcangle_it4.18
r_mcangle_other4.18
r_scbond_it3.8
r_scbond_other3.799
r_mcbond_it2.908
r_mcbond_other2.901
r_angle_refined_deg2.002
r_angle_other_deg1.139
r_chiral_restr0.162
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3975
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing