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The Structure and conformation of Lys-63 linked tetra-ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.88 57.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.882 α = 90 b = 105.882 β = 90 c = 105.882 γ = 90
Symmetry Space Group P 21 3
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 2008-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90020 APS 14-BM-C
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 1.96 25.68 99.6 0.081 54.367 42.9 28616
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 1.96 2.01 100 0.902 43.1
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 1UBQ 1.96 25.68 27141 1448 99.58 0.1882 0.18569 0.1926 0.23611 0.2396 RANDOM 42.133
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.892 r_dihedral_angle_4_deg 19.941 r_dihedral_angle_3_deg 16.208 r_dihedral_angle_1_deg 6.573 r_scangle_it 4.225 r_scbond_it 2.923 r_angle_refined_deg 1.885 r_mcangle_it 1.634 r_mcbond_it 1.271 r_angle_other_deg 1.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.892 r_dihedral_angle_4_deg 19.941 r_dihedral_angle_3_deg 16.208 r_dihedral_angle_1_deg 6.573 r_scangle_it 4.225 r_scbond_it 2.923 r_angle_refined_deg 1.885 r_mcangle_it 1.634 r_mcbond_it 1.271 r_angle_other_deg 1.008 r_symmetry_vdw_refined 0.378 r_mcbond_other 0.348 r_symmetry_vdw_other 0.291 r_nbd_refined 0.246 r_symmetry_hbond_refined 0.238 r_xyhbond_nbd_refined 0.211 r_nbd_other 0.206 r_metal_ion_refined 0.195 r_nbtor_refined 0.175 r_chiral_restr 0.128 r_xyhbond_nbd_other 0.103 r_nbtor_other 0.089 r_symmetry_metal_ion_refined 0.046 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2404 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling