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Crystal structure of the mouse TAB3-NZF in complex with Lys63-linked di-ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A9J PDB ENTRY 3A9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100mM Bis-Tris-HCl (pH 6.5), 21% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.8 31.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.9 α = 90 b = 71.018 β = 90 c = 71.562 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 100 CCD RAYONIX MX225HE mirrors 2009-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 1.4 50 97.8 0.05 36.8 30844 30844
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) 1.4 1.42 93.5 0.347 2.78
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3A9J 1.4 25.72 28621 1513 97.9 0.18875 0.18717 0.1869 0.21789 0.2185 RANDOM 18.054
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] -0.27 -0.03 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.902 r_dihedral_angle_4_deg 18.584 r_dihedral_angle_3_deg 14.668 r_dihedral_angle_1_deg 6.301 r_sphericity_free 5.226 r_scangle_it 4.971 r_scbond_it 4.605 r_rigid_bond_restr 4.417 r_sphericity_bonded 3.857 r_mcangle_it 2.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.902 r_dihedral_angle_4_deg 18.584 r_dihedral_angle_3_deg 14.668 r_dihedral_angle_1_deg 6.301 r_sphericity_free 5.226 r_scangle_it 4.971 r_scbond_it 4.605 r_rigid_bond_restr 4.417 r_sphericity_bonded 3.857 r_mcangle_it 2.103 r_angle_refined_deg 1.409 r_mcbond_it 1.294 r_nbtor_refined 0.314 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.203 r_symmetry_hbond_refined 0.196 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1468 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 1
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling