3TSV

crystal structure of the third PDZ domain of the human ZO-1 MAGUK protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LH5PDB ENTRY 3LH5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5293.1525% PEG 1500, 0.1M MMT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
1.6927.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.497α = 90
b = 45.117β = 90
c = 59.634γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.98935.9897.80.0515.13.266496649
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)
11.9892.1193.30.612.13.2995

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 3LH51.98935.985970597066397.620.273260.273260.268580.31526RANDOM36.873
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]
-1.631.180.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.914
r_dihedral_angle_4_deg21.73
r_dihedral_angle_3_deg18.291
r_dihedral_angle_1_deg5.928
r_scangle_it2.367
r_scbond_it1.347
r_angle_refined_deg1.165
r_mcangle_it1.122
r_mcbond_it0.606
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.914
r_dihedral_angle_4_deg21.73
r_dihedral_angle_3_deg18.291
r_dihedral_angle_1_deg5.928
r_scangle_it2.367
r_scbond_it1.347
r_angle_refined_deg1.165
r_mcangle_it1.122
r_mcbond_it0.606
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms721
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms

Software

Software
Software NamePurpose
SERGUIdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling