1TP3

PDZ3 domain of PSD-95 protein complexed with KKETPV peptide ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BE9PDB ENTRY 1BE9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.92951.0 M sodium citrate, 0.1 M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.663α = 90
b = 89.663β = 90
c = 89.663γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9923.9699.7611.588916891611
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.0699.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1BE91.9919.5718486848642399.720.23280.227880.22470.2961RANDOM25.567
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.029
r_scangle_it6.682
r_scbond_it4.129
r_angle_refined_deg2.721
r_mcangle_it2.599
r_mcbond_it1.618
r_angle_other_deg1.223
r_symmetry_vdw_refined0.398
r_symmetry_vdw_other0.358
r_nbd_other0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.029
r_scangle_it6.682
r_scbond_it4.129
r_angle_refined_deg2.721
r_mcangle_it2.599
r_mcbond_it1.618
r_angle_other_deg1.223
r_symmetry_vdw_refined0.398
r_symmetry_vdw_other0.358
r_nbd_other0.28
r_symmetry_hbond_refined0.251
r_nbd_refined0.239
r_xyhbond_nbd_refined0.18
r_chiral_restr0.175
r_nbtor_other0.107
r_bond_refined_d0.038
r_gen_planes_refined0.013
r_gen_planes_other0.008
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms908
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
d*TREKdata scaling
XTALVIEWrefinement