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Oxidized dimeric PICK1 PDZ 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 8.4 289 20% (w/v) PEG3350, 0.2M Lithium Citrate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.93 36.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.26 α = 90 b = 51.79 β = 90 c = 80.83 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 2.2 80.85 99.9 0.067 10.3 9.2 11020 11020 36.778
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) 2.2 2.32 99.9 0.417 1.8 9.1 1571
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 2.2 80.85 11020 9933 1082 99.81 0.20848 0.20565 0.2022 0.23463 0.2325 RANDOM 32.275
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.154 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_1_deg 5.621 r_dihedral_angle_4_deg 4.215 r_scangle_it 1.88 r_scbond_it 1.178 r_angle_refined_deg 1.124 r_mcangle_it 0.853 r_mcbond_it 0.776 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.154 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_1_deg 5.621 r_dihedral_angle_4_deg 4.215 r_scangle_it 1.88 r_scbond_it 1.178 r_angle_refined_deg 1.124 r_mcangle_it 0.853 r_mcbond_it 0.776 r_nbtor_refined 0.295 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.161 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.068 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 1622 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 6
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling