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Crystal structure of CYLD USP domain (C596A) in complex with Lys63-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 7 293 0.2M sodium malonate buffer, 18% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.017 α = 103.49 b = 65.657 β = 89.86 c = 69.821 γ = 90.61
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 2013-06-28 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 3.1 50 96.7 0.101 15888 15888
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 3.1 3.15 91.8 0.399 2.06
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2VHF and 1UBQ 3.1 41.89 15888 14407 758 96.7 0.19098 0.18816 0.24559 0.2275 RANDOM 60.137
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] -2.33 -0.87 -0.32 3.88 0.56 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.731 r_dihedral_angle_3_deg 20.6 r_dihedral_angle_4_deg 19.655 r_long_range_B_refined 7.494 r_long_range_B_other 7.494 r_dihedral_angle_1_deg 6.682 r_scangle_other 4.582 r_mcangle_it 4.573 r_mcangle_other 4.572 r_mcbond_other 2.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.731 r_dihedral_angle_3_deg 20.6 r_dihedral_angle_4_deg 19.655 r_long_range_B_refined 7.494 r_long_range_B_other 7.494 r_dihedral_angle_1_deg 6.682 r_scangle_other 4.582 r_mcangle_it 4.573 r_mcangle_other 4.572 r_mcbond_other 2.704 r_mcbond_it 2.703 r_scbond_it 2.681 r_scbond_other 2.68 r_angle_refined_deg 1.363 r_angle_other_deg 0.869 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 7218 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling