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Oxidized dimeric PICK1 PDZ C46G mutant in complex with the carboxyl tail peptide of GluR2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PKU PDB ENTRY 2PKU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 20% (w/v) PEG4000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.02 39.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.45 α = 90 b = 54 β = 90 c = 92.38 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV++ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 46.62 96.8 0.064 7.6 4.4 4797 4797 77.041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.95 96.8 0.377 2 4.4 683
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PKU 2.8 46.62 4797 4307 465 96 0.24807 0.24305 0.2385 0.29504 0.2877 RANDOM 53.494
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] 6.83 -2.96 -3.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.168 r_dihedral_angle_3_deg 21.094 r_dihedral_angle_1_deg 5.932 r_dihedral_angle_4_deg 3.566 r_angle_refined_deg 1.31 r_scangle_it 1.072 r_scbond_it 0.675 r_mcangle_it 0.481 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.168 r_dihedral_angle_3_deg 21.094 r_dihedral_angle_1_deg 5.932 r_dihedral_angle_4_deg 3.566 r_angle_refined_deg 1.31 r_scangle_it 1.072 r_scbond_it 0.675 r_mcangle_it 0.481 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.286 r_mcbond_it 0.281 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.185 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 1545 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling