5OJ1

Penicillin Binding Protein 2x (PBP2x) from S.pneumoniae in complex with Oxacillin and a tetrasaccharide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K25 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52902.3-3M NaCl, 0.1M Na Acetate pH 4.5
Crystal Properties
Matthews coefficientSolvent content
3.7567.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.839α = 90
b = 100.839β = 90
c = 189.354γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97497ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.8548.721000.1920.0789.36.926783
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.8531001.70.71.37

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 REPLACEMENTTHROUGHOUT1K252.8587.3325437130399.940.170270.167290.22875RANDOM70.969
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.736
r_dihedral_angle_3_deg18.404
r_dihedral_angle_4_deg15.256
r_long_range_B_other10.596
r_long_range_B_refined10.595
r_dihedral_angle_1_deg8.259
r_mcangle_it7.621
r_mcangle_other7.62
r_scangle_other7.606
r_scbond_it5.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.736
r_dihedral_angle_3_deg18.404
r_dihedral_angle_4_deg15.256
r_long_range_B_other10.596
r_long_range_B_refined10.595
r_dihedral_angle_1_deg8.259
r_mcangle_it7.621
r_mcangle_other7.62
r_scangle_other7.606
r_scbond_it5.309
r_scbond_other5.292
r_mcbond_it5.146
r_mcbond_other5.144
r_angle_refined_deg1.761
r_angle_other_deg1.069
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.003
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 Atoms5178
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing