5OAU

Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae


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
Crystal Properties
Matthews coefficientSolvent content
3.5765.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.26α = 90
b = 100.26β = 90
c = 189.81γ = 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
12.6734.7899.30.10.097.53.531872
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)
12.672.899.10.570.481.73.3

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 REPLACEMENTTHROUGHOUT1k252.6734.7830573150699.880.175880.173450.22531RANDOM62.804
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]
-0.05-0.03-0.050.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.587
r_dihedral_angle_3_deg15.943
r_dihedral_angle_4_deg14.903
r_long_range_B_refined12.249
r_long_range_B_other12.247
r_scangle_other7.953
r_mcangle_it7.871
r_mcangle_other7.87
r_dihedral_angle_1_deg7.28
r_scbond_it5.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.587
r_dihedral_angle_3_deg15.943
r_dihedral_angle_4_deg14.903
r_long_range_B_refined12.249
r_long_range_B_other12.247
r_scangle_other7.953
r_mcangle_it7.871
r_mcangle_other7.87
r_dihedral_angle_1_deg7.28
r_scbond_it5.464
r_scbond_other5.464
r_mcbond_it5.259
r_mcbond_other5.259
r_angle_refined_deg1.742
r_angle_other_deg1.056
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.007
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 Atoms5131
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing