9SGD | pdb_00009sgd

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (26)


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
3.2962.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.239α = 90
b = 148.297β = 90
c = 98.144γ = 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
11.5743.5795.90.0530.99810.293.49473342.78
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)
11.571.66970.1730.2270.733.4

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-VALUE1.57143.56794667206795.9480.1770.17670.18930.20520.214344.83
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]
0.766-0.332-0.434
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.305
r_dihedral_angle_6_deg15.024
r_dihedral_angle_3_deg11.133
r_lrange_it7.79
r_lrange_other7.772
r_dihedral_angle_1_deg6.41
r_scangle_it6.08
r_scangle_other6.078
r_scbond_it4.178
r_scbond_other4.178
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.305
r_dihedral_angle_6_deg15.024
r_dihedral_angle_3_deg11.133
r_lrange_it7.79
r_lrange_other7.772
r_dihedral_angle_1_deg6.41
r_scangle_it6.08
r_scangle_other6.078
r_scbond_it4.178
r_scbond_other4.178
r_dihedral_angle_other_2_deg3.108
r_mcangle_it3.08
r_mcangle_other3.079
r_mcbond_it2.293
r_mcbond_other2.29
r_angle_refined_deg1.294
r_angle_other_deg0.456
r_symmetry_nbd_refined0.227
r_nbd_other0.217
r_nbd_refined0.216
r_symmetry_xyhbond_nbd_refined0.196
r_symmetry_nbd_other0.194
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.131
r_symmetry_nbtor_other0.077
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3624
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing