7RD0

Crystal structure of C. difficile penicillin-binding protein 3 in apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LP4 

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
3.2562.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.02α = 90
b = 114.22β = 90
c = 154.63γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-04-02MSINGLE 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
12.445.9899.90.0840.0930.0380.9928.35.729788
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)
12.42.4999.91.0051.1040.4530.7435.8

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 REPLACEMENTTHROUGHOUT5lp42.445.9828232152999.770.19150.18880.2412RANDOM59.413
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]
1.771.97-3.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.204
r_dihedral_angle_3_deg16.466
r_dihedral_angle_4_deg10.599
r_dihedral_angle_1_deg7.569
r_angle_refined_deg1.533
r_angle_other_deg1.236
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.204
r_dihedral_angle_3_deg16.466
r_dihedral_angle_4_deg10.599
r_dihedral_angle_1_deg7.569
r_angle_refined_deg1.533
r_angle_other_deg1.236
r_chiral_restr0.067
r_bond_refined_d0.008
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 Atoms3823
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms25

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MoRDaphasing