3H68

Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c)with two Zn2+ atoms originally soaked with cantharidin (which is present in the structure in the hydrolyzed form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S95 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP828910mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3347.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.175α = 90
b = 41.721β = 97.24
c = 105.172γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2008-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.98340ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.5401000.0910.09110.65.5954909549017
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.581000.4580.4581.52.47938

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1S951.538.24867278672787421000.188320.188320.183950.23232RANDOM20.782
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]
-0.351.28-0.571.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.02
r_dihedral_angle_4_deg14.028
r_dihedral_angle_3_deg13.479
r_dihedral_angle_1_deg6.194
r_sphericity_free5.038
r_scangle_it4.054
r_sphericity_bonded3.114
r_scbond_it2.756
r_mcangle_it1.827
r_angle_refined_deg1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.02
r_dihedral_angle_4_deg14.028
r_dihedral_angle_3_deg13.479
r_dihedral_angle_1_deg6.194
r_sphericity_free5.038
r_scangle_it4.054
r_sphericity_bonded3.114
r_scbond_it2.756
r_mcangle_it1.827
r_angle_refined_deg1.6
r_rigid_bond_restr1.584
r_mcbond_it1.202
r_chiral_restr0.105
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5056
Nucleic Acid Atoms
Solvent Atoms613
Heterogen Atoms64

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling