9SSE | pdb_00009sse

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Ampicillin - 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
3.362.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.275α = 90
b = 148.859β = 90
c = 99.386γ = 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
11.78848.1499.40.0870.9968.824.326699639.987
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)
11.7881.999.71.2210.4791.24.49

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-VALUE1.7948.13866996205299.3680.1690.16790.17840.1890.200840.046
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]
-0.1110.391-0.281
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.398
r_dihedral_angle_3_deg11.27
r_lrange_it8.179
r_lrange_other8.137
r_scangle_it7.195
r_scangle_other7.194
r_dihedral_angle_1_deg6.328
r_dihedral_angle_2_deg5.872
r_scbond_it4.646
r_scbond_other4.645
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.398
r_dihedral_angle_3_deg11.27
r_lrange_it8.179
r_lrange_other8.137
r_scangle_it7.195
r_scangle_other7.194
r_dihedral_angle_1_deg6.328
r_dihedral_angle_2_deg5.872
r_scbond_it4.646
r_scbond_other4.645
r_mcangle_other3.447
r_mcangle_it3.446
r_mcbond_it2.605
r_mcbond_other2.605
r_angle_refined_deg1.202
r_angle_other_deg0.422
r_nbd_refined0.213
r_symmetry_nbd_refined0.196
r_symmetry_nbd_other0.19
r_nbd_other0.189
r_nbtor_refined0.186
r_symmetry_xyhbond_nbd_refined0.142
r_xyhbond_nbd_refined0.127
r_symmetry_nbtor_other0.078
r_chiral_restr0.066
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3506
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms46

Software

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