2PZD

Crystal Structure of the HtrA2/Omi PDZ Domain Bound to a Phage-Derived Ligand (WTMFWV)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LCY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.62920.1 M sodium citrate, 1.0 M monoammonium dihydrogen phosphate, pH 5.6, VAPOR DIFFUSION, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.3663.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.105α = 90
b = 90.105β = 90
c = 83.516γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.975SSRLBL9-1

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
12.755099.80.07111.26.99406
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)
12.752.851000.5943.67.2901

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1LCY2.75208900889845399.980.210.2080.254RANDOM35.281
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]
-0.47-0.470.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.386
r_scangle_it3.977
r_mcangle_it3.788
r_scbond_it2.518
r_mcbond_it2.279
r_angle_refined_deg1.218
r_angle_other_deg0.768
r_nbd_other0.221
r_symmetry_vdw_refined0.215
r_nbd_refined0.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.386
r_scangle_it3.977
r_mcangle_it3.788
r_scbond_it2.518
r_mcbond_it2.279
r_angle_refined_deg1.218
r_angle_other_deg0.768
r_nbd_other0.221
r_symmetry_vdw_refined0.215
r_nbd_refined0.185
r_symmetry_vdw_other0.172
r_xyhbond_nbd_refined0.087
r_nbtor_other0.084
r_chiral_restr0.067
r_bond_refined_d0.012
r_symmetry_hbond_refined0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1678
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms8

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing