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N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDJ pdb entry 1LDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 276 27% PEG1500, 0.1M MIB, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 276K
Crystal Properties Matthews coefficient Solvent content 2.01 38.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.431 α = 90 b = 65.454 β = 104.73 c = 64.182 γ = 90
Symmetry Space Group C 1 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 77 CCD ADSC QUANTUM 315r 2010-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 50 96.2 0.09 0.09 3.7 86181 78739 3 2.605
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 88 0.413 0.413 2.6 3.3
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 1LDJ 1.5 50 86181 78739 4150 96.08 0.20738 0.20606 0.2029 0.23249 0.2304 RANDOM 22.829
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] 1.55 0.39 -1.48 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.223 r_dihedral_angle_4_deg 15.466 r_dihedral_angle_3_deg 13.349 r_scangle_it 8.137 r_scbond_it 4.674 r_dihedral_angle_1_deg 4.213 r_mcangle_it 3.399 r_rigid_bond_restr 2.458 r_mcbond_it 1.62 r_angle_refined_deg 0.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.223 r_dihedral_angle_4_deg 15.466 r_dihedral_angle_3_deg 13.349 r_scangle_it 8.137 r_scbond_it 4.674 r_dihedral_angle_1_deg 4.213 r_mcangle_it 3.399 r_rigid_bond_restr 2.458 r_mcbond_it 1.62 r_angle_refined_deg 0.915 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4690 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms
Software Software Software Name Purpose BSS data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing