3C5W

Complex between PP2A-specific methylesterase PME-1 and PP2A core enzyme


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IE3PP2A A subunit, PP2A C subunit, PME-1 monomer
experimental modelPDB 3C5VPP2A A subunit, PP2A C subunit, PME-1 monomer

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529025% w/v PEG3350, 100 mM ammonium citrate, and 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.1743.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.292α = 90
b = 54.839β = 110.87
c = 125.146γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.810098.60.09532062320623-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.995.70.42.9

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 REPLACEMENTTHROUGHOUTPP2A A subunit, PP2A C subunit, PME-1 monomer2.8501923519235101898.630.198440.195130.26338RANDOM44.744
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]
-3.32-1.391.390.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.029
r_dihedral_angle_3_deg18.005
r_dihedral_angle_4_deg16.99
r_dihedral_angle_1_deg5.123
r_angle_refined_deg1.087
r_scangle_it1.049
r_scbond_it0.633
r_mcangle_it0.445
r_nbtor_refined0.301
r_mcbond_it0.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.029
r_dihedral_angle_3_deg18.005
r_dihedral_angle_4_deg16.99
r_dihedral_angle_1_deg5.123
r_angle_refined_deg1.087
r_scangle_it1.049
r_scbond_it0.633
r_mcangle_it0.445
r_nbtor_refined0.301
r_mcbond_it0.249
r_nbd_refined0.194
r_symmetry_hbond_refined0.155
r_symmetry_vdw_refined0.154
r_xyhbond_nbd_refined0.13
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6441
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing