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Crystal Structure of tandem WW domains of ITCH in complex with TXNIP peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RRE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 30% PEG4000, 0.2 M magnesium chloride, 0.1 M TRIS
Crystal Properties Matthews coefficient Solvent content 2.3 46.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.277 α = 90 b = 62.26 β = 90 c = 67.815 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9791829 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.4 45.86 99.9 0.043 0.046 0.017 1 25.1 7.1 24240
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 100 0.927 1.008 0.395 0.807 2 6.5 1191
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4RRE 1.4 45.86 23096 1144 99.87 0.15479 0.15336 0.18374 0.1912 RANDOM 24.151
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] -0.91 1.59 -0.68
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.173 r_dihedral_angle_2_deg 24.81 r_sphericity_bonded 13.914 r_dihedral_angle_4_deg 11.017 r_dihedral_angle_3_deg 8.962 r_dihedral_angle_1_deg 5.573 r_long_range_B_refined 4.928 r_long_range_B_other 4.909 r_mcangle_it 4.756 r_mcangle_other 4.75
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.173 r_dihedral_angle_2_deg 24.81 r_sphericity_bonded 13.914 r_dihedral_angle_4_deg 11.017 r_dihedral_angle_3_deg 8.962 r_dihedral_angle_1_deg 5.573 r_long_range_B_refined 4.928 r_long_range_B_other 4.909 r_mcangle_it 4.756 r_mcangle_other 4.75 r_scangle_other 4.009 r_mcbond_it 3.532 r_mcbond_other 3.522 r_scbond_it 3.095 r_scbond_other 3.092 r_rigid_bond_restr 2.34 r_angle_refined_deg 1.767 r_angle_other_deg 1.079 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 785 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing