☰ Navigation Tabs
Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NEX PDB ENTRY 1NEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 1.5 M Ammonium sulfate, 100mM Tris pH 8.5, 15% glycerol, 1mM SCF-I2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.87 68.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.281 α = 90 b = 108.281 β = 90 c = 165.594 γ = 120
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 4 Si(111) double crystal monochromator, Bent cylindrical Si mirror (Rh coating) 2004-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 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 2.6 93.66 99.8 0.058 24.3 5.5 66846 66846
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) 2.6 2.688 100 0.435 3.6 5.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NEX 2.6 93.66 63268 3375 99.76 0.21334 0.21058 0.26648 0.2035 RANDOM 54.854
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] 1.86 0.93 1.86 -2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.318 r_dihedral_angle_4_deg 22.37 r_dihedral_angle_3_deg 21.01 r_dihedral_angle_1_deg 7.468 r_scangle_it 3.836 r_scbond_it 2.422 r_angle_refined_deg 1.968 r_mcangle_it 1.479 r_mcbond_it 0.784 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.318 r_dihedral_angle_4_deg 22.37 r_dihedral_angle_3_deg 21.01 r_dihedral_angle_1_deg 7.468 r_scangle_it 3.836 r_scbond_it 2.422 r_angle_refined_deg 1.968 r_mcangle_it 1.479 r_mcbond_it 0.784 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9329 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing