7RCW

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


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, and 0.1 M Na Citrate pH 5.6
Crystal Properties
Matthews coefficientSolvent content
4.2170.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.91α = 90
b = 200.19β = 100.11
c = 70.68γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-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
135090.20.1150.1320.0630.9899.23.630882
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)
133.1686.10.6590.7550.3580.7743.6

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 REPLACEMENTTHROUGHOUT6G9F35029337150589.770.19980.19680.2596RANDOM64.274
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]
-0.1-3.283.33-1.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.801
r_dihedral_angle_3_deg18.505
r_dihedral_angle_4_deg18.28
r_dihedral_angle_1_deg7.561
r_angle_refined_deg1.54
r_angle_other_deg1.19
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.801
r_dihedral_angle_3_deg18.505
r_dihedral_angle_4_deg18.28
r_dihedral_angle_1_deg7.561
r_angle_refined_deg1.54
r_angle_other_deg1.19
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6430
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MoRDaphasing