7O4A

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


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
4.6673.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.688α = 90
b = 178.688β = 90
c = 223.652γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97925ALBAXALOC

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
13.02847.39795.10.3280.05814.332.126360
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)
13.0283.3062.930.468

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5TRO3.02847.39426360133963.3030.2150.21160.277884.766
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]
0.6510.3260.651-2.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.46
r_dihedral_angle_3_deg22.176
r_dihedral_angle_4_deg19.332
r_lrange_other14.25
r_lrange_it14.248
r_mcangle_it11.038
r_mcangle_other11.038
r_scangle_it10.062
r_scangle_other10.061
r_dihedral_angle_1_deg7.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.46
r_dihedral_angle_3_deg22.176
r_dihedral_angle_4_deg19.332
r_lrange_other14.25
r_lrange_it14.248
r_mcangle_it11.038
r_mcangle_other11.038
r_scangle_it10.062
r_scangle_other10.061
r_dihedral_angle_1_deg7.248
r_mcbond_it7.006
r_mcbond_other6.993
r_scbond_it6.283
r_scbond_other6.283
r_angle_refined_deg1.543
r_angle_other_deg1.174
r_nbd_other0.301
r_symmetry_xyhbond_nbd_refined0.29
r_nbd_refined0.22
r_symmetry_nbd_refined0.207
r_symmetry_nbd_other0.195
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.164
r_ncsr_local_group_10.13
r_symmetry_nbtor_other0.081
r_chiral_restr0.059
r_symmetry_xyhbond_nbd_other0.021
r_xyhbond_nbd_other0.008
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7840
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing