3HPK

Oxidized dimeric PICK1 PDZ in complex with the carboxyl tail peptide of GluR2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.428920% (w/v) PEG3350, 0.2M Lithium Citrate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.9336.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.26α = 90
b = 51.79β = 90
c = 80.83γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.280.8599.90.06710.39.2110201102036.778
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)
2.22.3299.90.4171.89.11571

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2PKU2.280.85110209933108299.810.208480.205650.23463RANDOM32.275
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]
0.35-0.14-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.154
r_dihedral_angle_3_deg14.664
r_dihedral_angle_1_deg5.621
r_dihedral_angle_4_deg4.215
r_scangle_it1.88
r_scbond_it1.178
r_angle_refined_deg1.124
r_mcangle_it0.853
r_mcbond_it0.776
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.154
r_dihedral_angle_3_deg14.664
r_dihedral_angle_1_deg5.621
r_dihedral_angle_4_deg4.215
r_scangle_it1.88
r_scbond_it1.178
r_angle_refined_deg1.124
r_mcangle_it0.853
r_mcbond_it0.776
r_nbtor_refined0.295
r_nbd_refined0.205
r_symmetry_vdw_refined0.161
r_symmetry_hbond_refined0.159
r_xyhbond_nbd_refined0.124
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1622
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms6

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling