2H2C

Crystal Structure of ZO-1 PDZ1 Bound to a Phage-Derived Ligand (WRRTTWV)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H3MPDB Entry: 2H3M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.62920.1 M Sodium Acetate, 2 M sodium formate, pH 4.6, VAPOR DIFFUSION, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.8957.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.591α = 90
b = 51.591β = 90
c = 88.262γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.00ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125099.80.05929.85.89658
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.071000.314.75.5930

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: 2H3M2409647962945899.840.210.210.2090.225RANDOM52.385
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]
1.790.891.79-2.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.87
r_dihedral_angle_4_deg12.162
r_dihedral_angle_3_deg12.045
r_dihedral_angle_1_deg5.624
r_scangle_it3.112
r_scbond_it1.928
r_angle_refined_deg1.16
r_mcangle_it1.033
r_mcbond_it0.684
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.87
r_dihedral_angle_4_deg12.162
r_dihedral_angle_3_deg12.045
r_dihedral_angle_1_deg5.624
r_scangle_it3.112
r_scbond_it1.928
r_angle_refined_deg1.16
r_mcangle_it1.033
r_mcbond_it0.684
r_nbtor_refined0.297
r_nbd_refined0.192
r_symmetry_vdw_refined0.13
r_xyhbond_nbd_refined0.107
r_chiral_restr0.084
r_symmetry_hbond_refined0.057
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms825
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction