7RCY

Crystal structure of C. difficile penicillin-binding protein 2 in complex with ceftobiprole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6G9F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29315% PEG 4000, 0.2 M AmSO4, 0.1 M Na Citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
4.1870.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.7α = 90
b = 196.39β = 105.66
c = 70.97γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
1353.8483.90.0830.1030.060.9819.32.628449
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1681.60.5390.6770.4050.6752.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6g9f350.0126959148383.470.21040.20730.2664RANDOM78.726
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]
-2.123.08-1.391.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.115
r_dihedral_angle_4_deg19.091
r_dihedral_angle_3_deg18.918
r_dihedral_angle_1_deg7.257
r_angle_refined_deg1.466
r_angle_other_deg1.239
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.115
r_dihedral_angle_4_deg19.091
r_dihedral_angle_3_deg18.918
r_dihedral_angle_1_deg7.257
r_angle_refined_deg1.466
r_angle_other_deg1.239
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6479
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MoRDaphasing