9SG9 | pdb_00009sg9

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (6)


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
3.2962.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.655α = 90
b = 148.242β = 90
c = 98.83γ = 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
11.884497.60.0660.9988.393.95657856.7
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)
11.881.99980.2930.0910.483.9

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-VALUE1.8843.99856519203697.5390.1790.17790.18660.22170.227665.819
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]
-2.1231.1480.974
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.397
r_dihedral_angle_3_deg11.971
r_lrange_other9.183
r_lrange_it9.178
r_scangle_it7.442
r_scangle_other7.333
r_dihedral_angle_2_deg7.013
r_dihedral_angle_1_deg6.626
r_scbond_it4.937
r_scbond_other4.845
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.397
r_dihedral_angle_3_deg11.971
r_lrange_other9.183
r_lrange_it9.178
r_scangle_it7.442
r_scangle_other7.333
r_dihedral_angle_2_deg7.013
r_dihedral_angle_1_deg6.626
r_scbond_it4.937
r_scbond_other4.845
r_mcangle_it4.56
r_mcangle_other4.56
r_mcbond_it3.377
r_mcbond_other3.376
r_angle_refined_deg1.294
r_angle_other_deg0.452
r_symmetry_nbd_refined0.224
r_symmetry_xyhbond_nbd_refined0.21
r_nbd_refined0.209
r_symmetry_nbd_other0.191
r_nbd_other0.184
r_nbtor_refined0.181
r_dihedral_angle_other_2_deg0.152
r_xyhbond_nbd_refined0.152
r_symmetry_nbtor_other0.077
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3488
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing