2REY

Crystal structure of the PDZ domain of human dishevelled 2 (homologous to Drosophila dsh)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L6OPDB entry 1L6O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.2M Ammonium acetate, 0.1M Bis-tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8633.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.644α = 90
b = 69.644β = 90
c = 57.54γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.95370SLSX10SA

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
11.5534.8299.60.0460.04615.314.91244612446
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)
11.551.6196.10.4680.4685.612.2

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 REPLACEMENTTHROUGHOUTPDB entry 1L6O1.5534.82118181181859999.850.212170.212170.210810.23982RANDOM22.157
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]
0.650.320.65-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.743
r_dihedral_angle_4_deg21.367
r_dihedral_angle_3_deg14.126
r_scangle_it7.61
r_dihedral_angle_1_deg6.138
r_scbond_it6.08
r_mcangle_it4.451
r_mcbond_it3.656
r_angle_refined_deg1.549
r_mcbond_other1.437
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.743
r_dihedral_angle_4_deg21.367
r_dihedral_angle_3_deg14.126
r_scangle_it7.61
r_dihedral_angle_1_deg6.138
r_scbond_it6.08
r_mcangle_it4.451
r_mcbond_it3.656
r_angle_refined_deg1.549
r_mcbond_other1.437
r_angle_other_deg0.932
r_symmetry_vdw_other0.257
r_symmetry_vdw_refined0.246
r_symmetry_hbond_refined0.212
r_nbd_refined0.188
r_nbd_other0.185
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.133
r_chiral_restr0.093
r_nbtor_other0.09
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms668
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing