7O4B

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291.15sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.6165.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.649α = 90
b = 180.649β = 90
c = 223.466γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 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
12.59347.51396.30.1470.0322.124.745182
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)
12.5932.8462.1630.42

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-VALUE5TRO2.59347.50545181231867.4270.2070.20480.241563.226
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]
-0.084-0.042-0.0840.273
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.978
r_dihedral_angle_3_deg20.416
r_dihedral_angle_4_deg19.05
r_lrange_other11.96
r_lrange_it11.957
r_scangle_it9.043
r_scangle_other9.019
r_mcangle_it8.623
r_mcangle_other8.623
r_dihedral_angle_1_deg7.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.978
r_dihedral_angle_3_deg20.416
r_dihedral_angle_4_deg19.05
r_lrange_other11.96
r_lrange_it11.957
r_scangle_it9.043
r_scangle_other9.019
r_mcangle_it8.623
r_mcangle_other8.623
r_dihedral_angle_1_deg7.014
r_scbond_it5.866
r_scbond_other5.825
r_mcbond_it5.673
r_mcbond_other5.664
r_angle_refined_deg1.566
r_angle_other_deg1.208
r_symmetry_xyhbond_nbd_refined0.427
r_nbd_other0.215
r_nbd_refined0.207
r_symmetry_nbd_other0.191
r_symmetry_nbd_refined0.182
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.155
r_chiral_restr_other0.142
r_ncsr_local_group_10.114
r_symmetry_nbtor_other0.08
r_chiral_restr0.065
r_symmetry_xyhbond_nbd_other0.023
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7755
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing