9SSI | pdb_00009ssi

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Cefditoren - 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
3.3162.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.941α = 90
b = 149.052β = 90
c = 98.802γ = 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
11.63948.4897.80.0770.99810.014.298559835.213
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)
11.6391.7498.91.8140.2310.674.13

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-VALUE1.6448.47185598214597.7850.1750.17380.18670.20350.214336.003
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]
0.64-0.559-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.455
r_dihedral_angle_6_deg15.653
r_dihedral_angle_3_deg11.223
r_lrange_it7.995
r_lrange_other7.853
r_dihedral_angle_1_deg6.547
r_scangle_it5.469
r_scangle_other5.468
r_scbond_it3.602
r_scbond_other3.601
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.455
r_dihedral_angle_6_deg15.653
r_dihedral_angle_3_deg11.223
r_lrange_it7.995
r_lrange_other7.853
r_dihedral_angle_1_deg6.547
r_scangle_it5.469
r_scangle_other5.468
r_scbond_it3.602
r_scbond_other3.601
r_mcangle_other2.361
r_mcangle_it2.36
r_mcbond_it1.755
r_mcbond_other1.752
r_angle_refined_deg1.272
r_angle_other_deg0.446
r_nbd_refined0.217
r_symmetry_nbd_other0.196
r_nbtor_refined0.186
r_symmetry_xyhbond_nbd_refined0.173
r_nbd_other0.163
r_xyhbond_nbd_refined0.162
r_symmetry_nbd_refined0.127
r_dihedral_angle_other_2_deg0.101
r_symmetry_nbtor_other0.078
r_chiral_restr0.072
r_symmetry_xyhbond_nbd_other0.023
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 Atoms570
Heterogen Atoms60

Software

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