9SG7 | pdb_00009sg7

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (11)


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
3.362.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.018α = 90
b = 148.677β = 90
c = 98.652γ = 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
11.5344.1495.80.0510.99910.54.110272239.27
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)
11.531.6393.41.80.2440.654

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-VALUE1.53444.134102528204296.4010.1770.17620.18890.19510.203838.296
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]
-0.6920.734-0.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.586
r_dihedral_angle_other_2_deg13.094
r_dihedral_angle_3_deg10.915
r_dihedral_angle_2_deg9.049
r_lrange_it7.563
r_lrange_other7.473
r_dihedral_angle_1_deg6.653
r_scangle_it5.483
r_scangle_other5.482
r_scbond_it3.651
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.586
r_dihedral_angle_other_2_deg13.094
r_dihedral_angle_3_deg10.915
r_dihedral_angle_2_deg9.049
r_lrange_it7.563
r_lrange_other7.473
r_dihedral_angle_1_deg6.653
r_scangle_it5.483
r_scangle_other5.482
r_scbond_it3.651
r_scbond_other3.651
r_mcangle_it2.492
r_mcangle_other2.492
r_mcbond_other1.902
r_mcbond_it1.901
r_angle_refined_deg1.286
r_angle_other_deg0.458
r_nbd_refined0.215
r_nbd_other0.204
r_symmetry_nbd_other0.195
r_nbtor_refined0.183
r_symmetry_xyhbond_nbd_refined0.182
r_symmetry_nbd_refined0.151
r_xyhbond_nbd_refined0.139
r_symmetry_nbtor_other0.077
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3616
Nucleic Acid Atoms
Solvent Atoms511
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing