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Structure of the SdeA DUB Domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1 M Tris:HCl, 3.0 M Sodium Chloride
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.192 α = 90 b = 64.192 β = 90 c = 120.717 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 MARMOSAIC 300 mm CCD 2015-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.979 APS 23-ID-B
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 2.55 50 90.8 0.166 11.1 10.8 18407
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.59 100 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2.64 40.89 15497 843 99.98 0.18702 0.18437 0.1899 0.23599 0.241 RANDOM 37.372
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.77 r_dihedral_angle_4_deg 19.079 r_dihedral_angle_3_deg 17.509 r_long_range_B_refined 6.935 r_long_range_B_other 6.934 r_dihedral_angle_1_deg 6.395 r_scangle_other 5.329 r_mcangle_it 3.802 r_mcangle_other 3.801 r_scbond_it 3.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.77 r_dihedral_angle_4_deg 19.079 r_dihedral_angle_3_deg 17.509 r_long_range_B_refined 6.935 r_long_range_B_other 6.934 r_dihedral_angle_1_deg 6.395 r_scangle_other 5.329 r_mcangle_it 3.802 r_mcangle_other 3.801 r_scbond_it 3.348 r_scbond_other 3.311 r_mcbond_it 2.484 r_mcbond_other 2.484 r_angle_refined_deg 1.658 r_angle_other_deg 1.054 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3782 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing