9SSF | pdb_00009ssf

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Methicillin - Streptococcus pneumoniae R6


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
3.362.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.517α = 90
b = 147.979β = 90
c = 99.597γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2021-02-01MSINGLE 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
11.92749.896.70.1230.9967.584.575208645.01
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)
11.9272.0496.92.450.220.64.63

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-VALUE1.93149.79950441201993.7880.2070.20630.21390.23180.241450.876
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]
0.065-0.6170.551
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.385
r_dihedral_angle_6_deg15.253
r_dihedral_angle_3_deg13.28
r_lrange_it9.037
r_lrange_other9.026
r_dihedral_angle_1_deg7.041
r_scangle_it7.029
r_scangle_other7.028
r_scbond_it4.597
r_scbond_other4.596
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.385
r_dihedral_angle_6_deg15.253
r_dihedral_angle_3_deg13.28
r_lrange_it9.037
r_lrange_other9.026
r_dihedral_angle_1_deg7.041
r_scangle_it7.029
r_scangle_other7.028
r_scbond_it4.597
r_scbond_other4.596
r_mcangle_it4.54
r_mcangle_other4.533
r_mcbond_other3.142
r_mcbond_it3.141
r_angle_refined_deg1.292
r_angle_other_deg0.457
r_symmetry_xyhbond_nbd_refined0.263
r_nbd_refined0.211
r_symmetry_nbd_other0.188
r_symmetry_nbd_refined0.185
r_nbtor_refined0.183
r_nbd_other0.155
r_xyhbond_nbd_refined0.149
r_symmetry_nbtor_other0.078
r_chiral_restr0.067
r_xyhbond_nbd_other0.021
r_bond_refined_d0.007
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 Atoms3514
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms50

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARP/wARPmodel building
Cootmodel building
REFMACrefinement