3CC0

The Dvl2 PDZ Domain in Complex with the N3 Inhibitory Peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172921.0 M Ammonium citrate tribasic, 0.1 M BIS-TRIS propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
1.9938.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.617α = 90
b = 52.617β = 90
c = 171.098γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

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
11.755099.50.05819.83.826928
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)
11.751.8199.40.4363.53.7

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 REPLACEMENTTHROUGHOUT3CBX1.752025423134899.60.190.1880.238RANDOM23.02
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]
-0.43-0.22-0.430.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.951
r_dihedral_angle_4_deg14.912
r_dihedral_angle_3_deg13.04
r_dihedral_angle_1_deg6.602
r_scangle_it5.302
r_mcangle_it4.174
r_scbond_it3.966
r_mcbond_it3.59
r_angle_refined_deg1.458
r_angle_other_deg0.878
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.951
r_dihedral_angle_4_deg14.912
r_dihedral_angle_3_deg13.04
r_dihedral_angle_1_deg6.602
r_scangle_it5.302
r_mcangle_it4.174
r_scbond_it3.966
r_mcbond_it3.59
r_angle_refined_deg1.458
r_angle_other_deg0.878
r_mcbond_other0.73
r_symmetry_vdw_other0.242
r_symmetry_vdw_refined0.21
r_nbd_refined0.192
r_nbd_other0.191
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.161
r_symmetry_hbond_refined0.134
r_chiral_restr0.086
r_nbtor_other0.083
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2299
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction