☰ Navigation Tabs
Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VHF PDB entry 2VHF and 1UBQ experimental model PDB 1UBQ PDB entry 2VHF and 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 50mM Tris-HCl buffer, 9% PEG4000, 100mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.676 α = 90 b = 49.788 β = 102.69 c = 71.003 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX225HE mirrors 2013-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00000 SPring-8 BL41XU
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 2.5 50 96.9 0.094 15549 15549
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 2.5 2.54 92.4 0.329 2.9
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 (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 2VHF and 1UBQ 2.5 50 15549 14287 766 96.97 0.18518 0.18191 0.1854 0.24722 0.2474 RANDOM 50.063
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] 2 0.45 -1.2 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.27 r_dihedral_angle_4_deg 18.156 r_dihedral_angle_3_deg 17.828 r_long_range_B_refined 9.021 r_long_range_B_other 9.015 r_scangle_other 6.439 r_dihedral_angle_1_deg 6.02 r_mcangle_it 5.364 r_mcangle_other 5.363 r_scbond_it 4.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.27 r_dihedral_angle_4_deg 18.156 r_dihedral_angle_3_deg 17.828 r_long_range_B_refined 9.021 r_long_range_B_other 9.015 r_scangle_other 6.439 r_dihedral_angle_1_deg 6.02 r_mcangle_it 5.364 r_mcangle_other 5.363 r_scbond_it 4.264 r_scbond_other 4.263 r_mcbond_it 3.306 r_mcbond_other 3.305 r_angle_refined_deg 1.6 r_angle_other_deg 0.855 r_chiral_restr 0.081 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3617 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling