3TSZ

crystal structure of PDZ3-SH3-GUK core module from human ZO-1 in complex with 12mer peptide from human JAM-A cytoplasmic tail


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4293.159% PEG 3350, 0.1 M Sodium Malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.4649.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.5α = 90
b = 49.7β = 101.1
c = 91.8γ = 90
Symmetry
Space GroupP 1 21 1

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
12.590.196.10.08115.085.41507715077
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)
12.52.5774.60.5531.632.4849

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 3LH52.50290.081355713557152096.160.246750.246750.239660.30889RANDOM55.845
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]
0.38-0.76-0.22-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.217
r_dihedral_angle_4_deg20.848
r_dihedral_angle_3_deg17.59
r_dihedral_angle_1_deg5.265
r_scangle_it1.393
r_angle_refined_deg1.058
r_scbond_it0.784
r_mcangle_it0.62
r_mcbond_it0.33
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.217
r_dihedral_angle_4_deg20.848
r_dihedral_angle_3_deg17.59
r_dihedral_angle_1_deg5.265
r_scangle_it1.393
r_angle_refined_deg1.058
r_scbond_it0.784
r_mcangle_it0.62
r_mcbond_it0.33
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2809
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms

Software

Software
Software NamePurpose
SERGUIdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling