7OK9

Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with pentaglycine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7O49 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291.15DL-malic acid
Crystal Properties
Matthews coefficientSolvent content
3.9668.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 313.993α = 90
b = 198.186β = 90
c = 220.903γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target

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
13.35749.32189.10.6740.1957.512.886448
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)
13.3573.7562.7230.785

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 REPLACEMENTTHROUGHOUT7O493.3649.3282133431344.140.2320.23010.2669RANDOM97.202
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]
3.022.15-5.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.621
r_dihedral_angle_3_deg20.965
r_dihedral_angle_4_deg14.743
r_dihedral_angle_1_deg6.37
r_angle_refined_deg1.558
r_angle_other_deg1.439
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.621
r_dihedral_angle_3_deg20.965
r_dihedral_angle_4_deg14.743
r_dihedral_angle_1_deg6.37
r_angle_refined_deg1.558
r_angle_other_deg1.439
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms47732
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms178

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing