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Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDK PDB ENTRY 1LDK and 1UMH experimental model PDB 1UMH PDB ENTRY 1LDK and 1UMH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 293 2.0M ammonium sulphate, 0.1M sodium citrate, 30mM chitobiose, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.41 63.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.408 α = 90 b = 106.408 β = 90 c = 109.854 γ = 120
Symmetry Space Group P 32 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 Bruker DIP-6040 2004-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 2.4 109.8 97.7 0.045 18.1 5.4 27964 52.83
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) 2.4 2.49 93 0.327 2.7 2.9
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 SIR-AS, MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LDK and 1UMH 2.4 53.22 26521 1425 97.76 0.23605 0.23334 0.2299 0.29136 0.2843 RANDOM 66.935
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] 0.11 0.06 0.11 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.366 r_dihedral_angle_3_deg 19.265 r_dihedral_angle_4_deg 19.142 r_dihedral_angle_1_deg 6.382 r_scangle_it 2.425 r_scbond_it 1.406 r_angle_refined_deg 1.351 r_mcangle_it 1.226 r_mcbond_it 0.656 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.366 r_dihedral_angle_3_deg 19.265 r_dihedral_angle_4_deg 19.142 r_dihedral_angle_1_deg 6.382 r_scangle_it 2.425 r_scbond_it 1.406 r_angle_refined_deg 1.351 r_mcangle_it 1.226 r_mcbond_it 0.656 r_nbtor_refined 0.305 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3055 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHARP phasing