3V5E

Crystal structure of ClpP from Staphylococcus aureus in the active, extended conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QWDPDB entry 3QWD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293200 mM Sodium malonate, 38% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4249.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.22α = 90
b = 94.86β = 97.74
c = 139.02γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
12.35096.10.06511.2113429612905822
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)
12.32.498.60.512.23

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3QWD2.348.2129058122589645396.130.202350.200840.23108RANDOM48.154
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]
0.22-0.190.1-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.346
r_sphericity_free26.41
r_dihedral_angle_3_deg13.923
r_dihedral_angle_4_deg12.522
r_sphericity_bonded6.22
r_dihedral_angle_1_deg4.754
r_rigid_bond_restr2.059
r_angle_refined_deg0.86
r_chiral_restr0.06
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.346
r_sphericity_free26.41
r_dihedral_angle_3_deg13.923
r_dihedral_angle_4_deg12.522
r_sphericity_bonded6.22
r_dihedral_angle_1_deg4.754
r_rigid_bond_restr2.059
r_angle_refined_deg0.86
r_chiral_restr0.06
r_bond_refined_d0.005
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19908
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms

Software

Software
Software NamePurpose
RemDAqdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing