6TIX

Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP296Crystals were grown in a condition containing 1 uL of 0.8 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 1 uL of reservoir solution (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000). The size of these crystals was optimised by three rounds of macroseeding into condition containing (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000 and 2 mM mecillinam)
Crystal Properties
Matthews coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.172α = 112.917
b = 84.035β = 95.306
c = 87.099γ = 104.566
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 2M2018-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8731ESRFID23-2

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
12.845.69392.90.1080.0970.9914.12.127215
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9596.70.4520.640.4520.6771.22.1

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-VALUE5LP42.845.69327076130892.4320.2310.2280.290266.303
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]
-4.63-8.426-6.1181.4244.6423.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.136
r_dihedral_angle_3_deg18.661
r_dihedral_angle_4_deg16.094
r_lrange_it8.632
r_lrange_other8.631
r_dihedral_angle_1_deg6.78
r_mcangle_it5.33
r_mcangle_other5.329
r_scangle_it4.728
r_scangle_other4.727
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.136
r_dihedral_angle_3_deg18.661
r_dihedral_angle_4_deg16.094
r_lrange_it8.632
r_lrange_other8.631
r_dihedral_angle_1_deg6.78
r_mcangle_it5.33
r_mcangle_other5.329
r_scangle_it4.728
r_scangle_other4.727
r_mcbond_it3.202
r_mcbond_other3.202
r_scbond_it2.711
r_scbond_other2.711
r_angle_refined_deg1.299
r_angle_other_deg1.091
r_symmetry_xyhbond_nbd_refined0.247
r_nbd_other0.237
r_symmetry_nbd_refined0.217
r_nbd_refined0.195
r_symmetry_nbd_other0.191
r_xyhbond_nbd_refined0.18
r_nbtor_refined0.162
r_symmetry_xyhbond_nbd_other0.121
r_ncsr_local_group_10.095
r_symmetry_nbtor_other0.078
r_chiral_restr0.046
r_chiral_restr_other0.035
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8166
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing