3L6X

Crystal structure of p120 catenin in complex with E-cadherin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XM9PDB entry 1XM9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.1 M Bis-Tris, 1.8 M Ammonium sulfate, 3% methanol, pH 5.6, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1460.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.403α = 90
b = 92.403β = 90
c = 171.89γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-32008-10-24SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9793APS19-BM

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
12.43599.90.05710.410.533911-3
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)
12.42.441000.3947.08810.61674

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 REPLACEMENTTHROUGHOUTPDB entry 1XM92.43233751170799.570.2030.2010.234RANDOM39.304
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]
1.210.61.21-1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.205
r_dihedral_angle_4_deg23.102
r_dihedral_angle_3_deg14.449
r_dihedral_angle_1_deg5.122
r_scangle_it3.6
r_scbond_it2.148
r_angle_refined_deg1.34
r_mcangle_it1.246
r_mcbond_it0.644
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.205
r_dihedral_angle_4_deg23.102
r_dihedral_angle_3_deg14.449
r_dihedral_angle_1_deg5.122
r_scangle_it3.6
r_scbond_it2.148
r_angle_refined_deg1.34
r_mcangle_it1.246
r_mcbond_it0.644
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3503
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms20

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling