7O49

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291.15D,L-malic acid
Crystal Properties
Matthews coefficientSolvent content
3.9268.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 311.862α = 90
b = 197.148β = 90
c = 221.596γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

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
13.0349.01589.80.1730.058118.9145321
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)
13.0333.4161.1950.401

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 REPLACEMENTTHROUGHOUT5TRO3.0349138083723755.240.21280.21110.2457RANDOM93.555
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]
-0.011.27-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.676
r_dihedral_angle_3_deg22.215
r_dihedral_angle_4_deg19.638
r_dihedral_angle_1_deg7.115
r_angle_refined_deg1.517
r_angle_other_deg1.213
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.676
r_dihedral_angle_3_deg22.215
r_dihedral_angle_4_deg19.638
r_dihedral_angle_1_deg7.115
r_angle_refined_deg1.517
r_angle_other_deg1.213
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms48489
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms167

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing