9SSH | pdb_00009ssh

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Ceftriaxone - 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
3.2762.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.062α = 90
b = 148.577β = 90
c = 98.589γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2021-02-24MSINGLE 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
11.79244.0298.60.0910.9989.154.676563742.832
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)
11.7921.994.72.340.210.544.77

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-VALUE1.79244.0265507229998.7160.1740.17280.18250.2050.21445.752
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]
0.8290.398-1.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.001
r_dihedral_angle_6_deg14.787
r_dihedral_angle_3_deg10.871
r_lrange_it8.202
r_lrange_other8.134
r_dihedral_angle_1_deg6.368
r_scangle_it6.036
r_scangle_other6.035
r_scbond_it3.947
r_scbond_other3.946
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.001
r_dihedral_angle_6_deg14.787
r_dihedral_angle_3_deg10.871
r_lrange_it8.202
r_lrange_other8.134
r_dihedral_angle_1_deg6.368
r_scangle_it6.036
r_scangle_other6.035
r_scbond_it3.947
r_scbond_other3.946
r_mcangle_other3.17
r_mcangle_it3.16
r_mcbond_it2.378
r_mcbond_other2.369
r_angle_refined_deg1.288
r_angle_other_deg0.452
r_nbd_refined0.213
r_symmetry_xyhbond_nbd_refined0.213
r_symmetry_nbd_refined0.206
r_nbd_other0.194
r_symmetry_nbd_other0.188
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.146
r_dihedral_angle_other_2_deg0.106
r_symmetry_nbtor_other0.077
r_chiral_restr0.067
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 Atoms3506
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms50

Software

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