3PDV

Structure of the PDlim2 PDZ domain in complex with the C-terminal 6-peptide extension of NS1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.22930.2M NaCl, 0.1M HEPES, 22.5% PEG3350, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.917α = 90
b = 81.917β = 90
c = 81.917γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS HTCMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.25099.7945884548

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.219.31454821599.790.200090.197990.2489RANDOM27.547
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_2_deg32.597
r_dihedral_angle_4_deg21.008
r_dihedral_angle_3_deg15.933
r_dihedral_angle_1_deg5.731
r_scangle_it2.558
r_scbond_it1.369
r_angle_refined_deg1.187
r_mcangle_it0.984
r_mcbond_it0.507
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.597
r_dihedral_angle_4_deg21.008
r_dihedral_angle_3_deg15.933
r_dihedral_angle_1_deg5.731
r_scangle_it2.558
r_scbond_it1.369
r_angle_refined_deg1.187
r_mcangle_it0.984
r_mcbond_it0.507
r_nbtor_refined0.294
r_nbd_refined0.197
r_metal_ion_refined0.185
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.167
r_symmetry_hbond_refined0.164
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_metal_ion_other
r_nbd_other
r_symmetry_vdw_other
r_angle_other_deg
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbtor_other
r_mcbond_other
r_gen_planes_other
r_bond_other_d
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms658
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms1

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling