5VZ2

Structure of ClpP from Staphylococcus aureus in complex with Acyldepsipeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3STA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5291.150.1 M NaOAc pH 4.5, 18-35% MPD, and 0.02 M CaCl2
Crystal Properties
Matthews coefficientSolvent content
2.7455.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.562α = 90
b = 126.131β = 93.42
c = 145.794γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMirrors2013-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.275097.30.06710.84155067
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.272.3590.40.3023.414353

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 REPLACEMENTTHROUGHOUT3STA2.2650153010199697.370.17960.17910.2187RANDOM37.633
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]
0.67-0.2-0.34-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.68
r_dihedral_angle_4_deg18.821
r_dihedral_angle_3_deg14.995
r_dihedral_angle_1_deg6.406
r_angle_refined_deg1.823
r_angle_other_deg1.047
r_chiral_restr0.102
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.68
r_dihedral_angle_4_deg18.821
r_dihedral_angle_3_deg14.995
r_dihedral_angle_1_deg6.406
r_angle_refined_deg1.823
r_angle_other_deg1.047
r_chiral_restr0.102
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19078
Nucleic Acid Atoms
Solvent Atoms679
Heterogen Atoms714

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection
PHASERphasing