9SG6 | pdb_00009sg6

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (10)


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
3.3363.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.483α = 90
b = 149.563β = 90
c = 99.467γ = 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
11.7444.396.70.0580.9999.884.27144348.21
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)
11.741.8497.71.80.2060.534.1

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-VALUE1.7444.29171392218596.6690.1760.17540.18540.20150.209951.83
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]
0.3050.42-0.725
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.225
r_dihedral_angle_3_deg11.844
r_dihedral_angle_2_deg11.459
r_lrange_it9.167
r_lrange_other9.115
r_scangle_it6.86
r_scangle_other6.859
r_dihedral_angle_other_2_deg6.791
r_dihedral_angle_1_deg6.696
r_scbond_it4.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.225
r_dihedral_angle_3_deg11.844
r_dihedral_angle_2_deg11.459
r_lrange_it9.167
r_lrange_other9.115
r_scangle_it6.86
r_scangle_other6.859
r_dihedral_angle_other_2_deg6.791
r_dihedral_angle_1_deg6.696
r_scbond_it4.49
r_scbond_other4.489
r_mcangle_other3.496
r_mcangle_it3.494
r_mcbond_it2.691
r_mcbond_other2.687
r_angle_refined_deg1.298
r_angle_other_deg0.461
r_nbd_refined0.208
r_symmetry_xyhbond_nbd_refined0.187
r_symmetry_nbd_other0.183
r_nbtor_refined0.18
r_symmetry_nbd_refined0.176
r_nbd_other0.164
r_xyhbond_nbd_refined0.133
r_symmetry_nbtor_other0.076
r_chiral_restr0.071
r_bond_refined_d0.008
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 Atoms3515
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing