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Crystal structure of the UBA domain of p62 and its interaction with ubiquitin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 100mM Citrate buffer pH5.0, 1.8M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.86 33.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.967 α = 90 b = 72.967 β = 90 c = 32.56 γ = 90
Symmetry Space Group P 43 21 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 315 2008-01-25 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2008-01-25 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97928, 0.97909, 0.96405, 0.98317 Photon Factory BL-5A
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 1.4 51.57 97 0.048 13.1 13.1 17371 17371
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) 1,2 1.4 1.45 82.5 0.356 11
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 1.4 50 17323 16435 888 96.93 0.17167 0.17167 0.17011 0.1994 0.20054 0.2083 RANDOM 11.036
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] -0.8 -0.8 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_3_deg 14.544 r_dihedral_angle_4_deg 13.295 r_sphericity_free 6.591 r_dihedral_angle_1_deg 4.326 r_scangle_it 4.179 r_sphericity_bonded 3.052 r_scbond_it 3.027 r_mcangle_it 2.024 r_rigid_bond_restr 1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_3_deg 14.544 r_dihedral_angle_4_deg 13.295 r_sphericity_free 6.591 r_dihedral_angle_1_deg 4.326 r_scangle_it 4.179 r_sphericity_bonded 3.052 r_scbond_it 3.027 r_mcangle_it 2.024 r_rigid_bond_restr 1.7 r_angle_refined_deg 1.697 r_mcbond_it 1.418 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 678 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 5
Software Software Software Name Purpose SERGUI data collection SOLVE phasing REFMAC refinement HKL-2000 data scaling