9SGC | pdb_00009sgc

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (24)


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
3.2862.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.62α = 90
b = 147.672β = 90
c = 97.898γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2024-06-25MSINGLE 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
11.5143.96960.040.99912.383.910619941.71
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)
11.511.6193.30.2920.1370.423.8

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-VALUE1.51443.952105780210796.3710.1840.18330.19650.21080.231446.631
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]
0.493-0.205-0.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg21.994
r_dihedral_angle_6_deg15.599
r_dihedral_angle_3_deg11.823
r_lrange_it8.872
r_lrange_other8.808
r_dihedral_angle_1_deg7.017
r_scangle_it6.471
r_scangle_other6.469
r_scbond_other4.325
r_scbond_it4.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg21.994
r_dihedral_angle_6_deg15.599
r_dihedral_angle_3_deg11.823
r_lrange_it8.872
r_lrange_other8.808
r_dihedral_angle_1_deg7.017
r_scangle_it6.471
r_scangle_other6.469
r_scbond_other4.325
r_scbond_it4.323
r_mcangle_it3.502
r_mcangle_other3.502
r_mcbond_it2.492
r_mcbond_other2.491
r_angle_refined_deg1.294
r_angle_other_deg0.455
r_dihedral_angle_other_2_deg0.232
r_symmetry_xyhbond_nbd_refined0.232
r_nbd_refined0.219
r_symmetry_nbd_other0.195
r_nbtor_refined0.185
r_nbd_other0.166
r_xyhbond_nbd_refined0.161
r_symmetry_nbd_refined0.147
r_symmetry_nbtor_other0.078
r_chiral_restr0.073
r_bond_refined_d0.008
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 Atoms3571
Nucleic Acid Atoms
Solvent Atoms459
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing