2H2B

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62920.1 M Sodium Acetate, 0.2 M Ammonium Sulfate, 30% PEG 2000 Monomethyl Ether, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.7254.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.425α = 90
b = 52.425β = 90
c = 92.932γ = 90
Symmetry
Space GroupP 41 21 2

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
11.615099.60.05231.97.317606
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)
11.611.6798.40.4013.75.81690

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: 2H3M1.630176641753889899.350.2050.2050.2030.232RANDOM27.636
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]
-0.1-0.10.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.276
r_dihedral_angle_4_deg19.697
r_dihedral_angle_3_deg11.458
r_dihedral_angle_1_deg5.983
r_scangle_it4.049
r_scbond_it2.503
r_mcangle_it1.642
r_angle_refined_deg1.358
r_mcbond_it1.181
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.276
r_dihedral_angle_4_deg19.697
r_dihedral_angle_3_deg11.458
r_dihedral_angle_1_deg5.983
r_scangle_it4.049
r_scbond_it2.503
r_mcangle_it1.642
r_angle_refined_deg1.358
r_mcbond_it1.181
r_nbtor_refined0.302
r_symmetry_hbond_refined0.273
r_symmetry_vdw_refined0.215
r_nbd_refined0.188
r_xyhbond_nbd_refined0.112
r_chiral_restr0.102
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms824
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction