7O4C

Crystal structure of PASTA domains of the Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OAU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291.15PEG 400 HEPES free acid/sodium hydroxide PEG 3000 Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.8857.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.972α = 90
b = 80.562β = 90
c = 90.422γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97918ALBAXALOC

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
11.5142.511000.0420.01230.81346753
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)
11.511.540.6870.193

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 REPLACEMENTTHROUGHOUT5OAU1.5140.3144285239999.990.16490.16270.2081RANDOM31.602
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]
1.05-0.99-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.558
r_rigid_bond_restr14.601
r_dihedral_angle_3_deg14.359
r_dihedral_angle_1_deg6.42
r_angle_other_deg1.689
r_angle_refined_deg1.613
r_chiral_restr0.082
r_bond_other_d0.018
r_bond_refined_d0.011
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.558
r_rigid_bond_restr14.601
r_dihedral_angle_3_deg14.359
r_dihedral_angle_1_deg6.42
r_angle_other_deg1.689
r_angle_refined_deg1.613
r_chiral_restr0.082
r_bond_other_d0.018
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1774
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing