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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 2E31 PDB ENTRY 2E31
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 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.942 α = 90 b = 109.816 β = 90 c = 153.04 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 Bruker DIP-6040 2004-01-29 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 3.5 152.5 85.2 0.103 7 2.6 12279 26.74
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) 3.5 3.63 79 0.225 4.1 2.1
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 PDB ENTRY 2E31 3.52 56.53 12269 651 89.7 0.22651 0.22259 0.218 0.29855 0.2888 RANDOM 51.038
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] -4.24 3.69 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.465 r_dihedral_angle_3_deg 24.536 r_dihedral_angle_4_deg 17.798 r_dihedral_angle_1_deg 9.509 r_scangle_it 2.992 r_angle_refined_deg 2.078 r_scbond_it 1.754 r_mcangle_it 1.321 r_mcbond_it 0.715 r_symmetry_hbond_refined 0.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.465 r_dihedral_angle_3_deg 24.536 r_dihedral_angle_4_deg 17.798 r_dihedral_angle_1_deg 9.509 r_scangle_it 2.992 r_angle_refined_deg 2.078 r_scbond_it 1.754 r_mcangle_it 1.321 r_mcbond_it 0.715 r_symmetry_hbond_refined 0.392 r_symmetry_vdw_refined 0.38 r_nbtor_refined 0.346 r_nbd_refined 0.307 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.127 r_bond_refined_d 0.022 r_gen_planes_refined 0.006 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 5970 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing