5EMB

Crystal structure of the SNX27 PDZ domain bound to the C-terminal phosphorylated PTHR PDZ binding motif


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29310% PEG1000, 10% PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.1943.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.57α = 90
b = 48.33β = 90
c = 56.177γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2015-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.70850Australian SynchrotronMX2

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
10.8531.26598.725.91490806
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.850.861002.062.813.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4Z8J0.8510.288390200099.860.123970.12370.13567RANDOM10.849
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]
0.06-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.747
r_dihedral_angle_2_deg27.101
r_dihedral_angle_4_deg20.853
r_rigid_bond_restr14.817
r_sphericity_bonded12.234
r_dihedral_angle_3_deg10.18
r_dihedral_angle_1_deg5.72
r_angle_refined_deg2.089
r_angle_other_deg0.888
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.747
r_dihedral_angle_2_deg27.101
r_dihedral_angle_4_deg20.853
r_rigid_bond_restr14.817
r_sphericity_bonded12.234
r_dihedral_angle_3_deg10.18
r_dihedral_angle_1_deg5.72
r_angle_refined_deg2.089
r_angle_other_deg0.888
r_chiral_restr0.106
r_bond_refined_d0.022
r_gen_planes_refined0.011
r_bond_other_d0.01
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms781
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing