5OJ0

Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae in complex with Cefepime


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52902.3-3.0 M NaCl, 0.1 M sodium acetate pH 4.5
Crystal Properties
Matthews coefficientSolvent content
3.4364.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.547α = 90
b = 99.547β = 90
c = 189.66γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97947ALBAXALOC

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
12.6639.2499.60.160.125.74.231872
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)
12.662.7699.60.80.694.3

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 REPLACEMENTTHROUGHOUT1k252.6639.2430354162199.930.174770.171650.23143RANDOM64.555
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]
-0.14-0.07-0.140.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.387
r_dihedral_angle_3_deg19.85
r_dihedral_angle_4_deg15.192
r_long_range_B_other13.936
r_long_range_B_refined13.935
r_scangle_other10.205
r_mcangle_it9.637
r_mcangle_other9.636
r_dihedral_angle_1_deg8.409
r_scbond_it7.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.387
r_dihedral_angle_3_deg19.85
r_dihedral_angle_4_deg15.192
r_long_range_B_other13.936
r_long_range_B_refined13.935
r_scangle_other10.205
r_mcangle_it9.637
r_mcangle_other9.636
r_dihedral_angle_1_deg8.409
r_scbond_it7.003
r_scbond_other7.002
r_mcbond_it6.611
r_mcbond_other6.606
r_angle_refined_deg2.013
r_angle_other_deg1.189
r_chiral_restr0.125
r_bond_refined_d0.018
r_gen_planes_refined0.009
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 Atoms5057
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
Cootmodel building