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Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ PDB ENTRY: 1UBQ, 1X23 experimental model PDB 1X23 PDB ENTRY: 1UBQ, 1X23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.1 292 0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.646 α = 90 b = 102.646 β = 90 c = 112.686 γ = 120
Symmetry Space Group P 3 2 1
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 210 2006-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0000 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.4 25 98.2 0.115 16.8 6.1 9814 9637 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.4 3.52 99.8 0.75 3.3 3.9 955
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY: 1UBQ, 1X23 3.4 25 9612 8650 962 98.09 0.284 0.28381 0.27984 0.2685 0.31882 0.3107 RANDOM 94.095
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] -3.19 -1.6 -3.19 4.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.848 r_dihedral_angle_3_deg 18.909 r_dihedral_angle_4_deg 12.395 r_dihedral_angle_1_deg 5.313 r_scangle_it 1.823 r_mcangle_it 1.281 r_scbond_it 1.253 r_angle_refined_deg 1.013 r_mcbond_it 0.834 r_symmetry_vdw_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.848 r_dihedral_angle_3_deg 18.909 r_dihedral_angle_4_deg 12.395 r_dihedral_angle_1_deg 5.313 r_scangle_it 1.823 r_mcangle_it 1.281 r_scbond_it 1.253 r_angle_refined_deg 1.013 r_mcbond_it 0.834 r_symmetry_vdw_refined 0.323 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.208 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3986 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling