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Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FQV PDB entry 1FQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.9 75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.7 α = 90 b = 148.7 β = 90 c = 98.8 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 173 IMAGE PLATE RIGAKU mirrors 2005-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97946 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 20 99.9 0.056 0.056 35 6.5 55849 55849 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 0.422 0.422 4 6 5513
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1FQV 2.3 20 52996 52996 2826 99.91 0.2028 0.2028 0.20178 0.22109 0.1992 RANDOM 57.844
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] -0.49 -0.25 -0.49 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.743 r_dihedral_angle_4_deg 19.929 r_dihedral_angle_3_deg 14.907 r_dihedral_angle_1_deg 5.151 r_scangle_it 4.186 r_mcangle_it 3.12 r_scbond_it 2.76 r_mcbond_it 2.008 r_angle_refined_deg 1.085 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.743 r_dihedral_angle_4_deg 19.929 r_dihedral_angle_3_deg 14.907 r_dihedral_angle_1_deg 5.151 r_scangle_it 4.186 r_mcangle_it 3.12 r_scbond_it 2.76 r_mcbond_it 2.008 r_angle_refined_deg 1.085 r_nbtor_refined 0.298 r_symmetry_vdw_refined 0.195 r_nbd_refined 0.189 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4377 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing