7AU9

Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 14)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HZR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629325% (w/v) polyethylene glycol 3,350, 0.1M Bis-Tris propane pH 6 and 1% (w/v) protamine sulphate
Crystal Properties
Matthews coefficientSolvent content
2.1743.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.7α = 90
b = 82.724β = 90
c = 88.538γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MMirrors2019-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.13760.44694.10.1210.0440.99912.98.621028
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.1372.34167.21.3110.4990.5821.67.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6HZR2.13760.4462102896073.4990.1960.19190.274348.565
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]
0.193-0.3130.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.65
r_dihedral_angle_4_deg20.769
r_dihedral_angle_3_deg17.404
r_lrange_it9.125
r_lrange_other9.06
r_dihedral_angle_1_deg7.636
r_scangle_it6.468
r_scangle_other6.467
r_mcangle_it5.852
r_mcangle_other5.848
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.65
r_dihedral_angle_4_deg20.769
r_dihedral_angle_3_deg17.404
r_lrange_it9.125
r_lrange_other9.06
r_dihedral_angle_1_deg7.636
r_scangle_it6.468
r_scangle_other6.467
r_mcangle_it5.852
r_mcangle_other5.848
r_scbond_it4.179
r_scbond_other4.178
r_mcbond_it3.904
r_mcbond_other3.903
r_angle_refined_deg1.57
r_angle_other_deg1.231
r_symmetry_xyhbond_nbd_refined0.234
r_nbd_other0.232
r_nbd_refined0.219
r_symmetry_nbd_refined0.214
r_symmetry_nbd_other0.19
r_xyhbond_nbd_refined0.164
r_nbtor_refined0.163
r_symmetry_nbtor_other0.079
r_chiral_restr0.063
r_symmetry_xyhbond_nbd_other0.061
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3731
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms32

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
STARANISOdata processing
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction