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Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases:SPOPMATHx-PucSBC1_pep2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HQH PDB entry 3HQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.795 α = 90 b = 43.69 β = 107.03 c = 86.819 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 CCD MARMOSAIC 225 mm CCD 2008-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
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 1.66 20 0.073 28.9 3.1 38876
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) 1 1.66 1.72 0.39 3.1 2.8 3796
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 3HQH 1.66 20 36636 1934 98.88 0.24721 0.24659 0.2447 0.25806 0.2551 RANDOM 18.01
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] 0.02 0.41 -0.74 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.159 r_dihedral_angle_4_deg 16.394 r_dihedral_angle_3_deg 11.741 r_dihedral_angle_1_deg 5.91 r_scangle_it 4.123 r_scbond_it 2.707 r_mcangle_it 1.706 r_angle_refined_deg 1.363 r_mcbond_it 1.235 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.159 r_dihedral_angle_4_deg 16.394 r_dihedral_angle_3_deg 11.741 r_dihedral_angle_1_deg 5.91 r_scangle_it 4.123 r_scbond_it 2.707 r_mcangle_it 1.706 r_angle_refined_deg 1.363 r_mcbond_it 1.235 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.267 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2168 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 10
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling