9SG8 | pdb_00009sg8

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (15)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BG1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229350MM HEPES PH 7.2, 3M NACL, 0.6-0.9M AMMONIUM SULFATE
Crystal Properties
Matthews coefficientSolvent content
3.2862.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.404α = 90
b = 148.533β = 90
c = 98.61γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2024-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.965459ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
11.8144.0595.80.0580.99811.313.86190449.02
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.9296.20.1390.4911.133.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.81144.04261903204495.9080.1610.16010.170.18090.186951.291
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]
-0.6280.801-0.173
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.426
r_dihedral_angle_3_deg11.302
r_lrange_it8.736
r_lrange_other8.699
r_dihedral_angle_1_deg6.609
r_dihedral_angle_2_deg6.59
r_scangle_it6.313
r_scangle_other6.311
r_scbond_it4.298
r_scbond_other4.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.426
r_dihedral_angle_3_deg11.302
r_lrange_it8.736
r_lrange_other8.699
r_dihedral_angle_1_deg6.609
r_dihedral_angle_2_deg6.59
r_scangle_it6.313
r_scangle_other6.311
r_scbond_it4.298
r_scbond_other4.297
r_mcangle_other3.429
r_mcangle_it3.425
r_dihedral_angle_other_2_deg2.932
r_mcbond_it2.589
r_mcbond_other2.576
r_angle_refined_deg1.289
r_angle_other_deg0.46
r_symmetry_xyhbond_nbd_refined0.258
r_nbd_refined0.208
r_symmetry_nbd_other0.184
r_nbtor_refined0.181
r_nbd_other0.163
r_symmetry_nbd_refined0.162
r_xyhbond_nbd_refined0.147
r_symmetry_nbtor_other0.075
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3515
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing