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Crystal structure of SdeA-modified ubiquitin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.596 α = 90 b = 81.073 β = 105.72 c = 51.287 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 PIXEL DECTRIS PILATUS 2M 2016-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00004 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.793 49.37 98 0.1224 0.995 8.24 3.4 22956
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.793 1.857 96 0.7956 0.535 1.38 3.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1UBQ 1.793 49.37 21807 1147 98.3 0.1907 0.18857 0.1983 0.23104 0.2388 RANDOM 19.991
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] -0.45 -0.28 1.41 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.819 r_dihedral_angle_4_deg 18.989 r_dihedral_angle_3_deg 13.986 r_long_range_B_refined 7.165 r_long_range_B_other 7.164 r_dihedral_angle_1_deg 6.828 r_scangle_other 5.053 r_scbond_it 3.257 r_scbond_other 3.244 r_mcangle_it 2.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.819 r_dihedral_angle_4_deg 18.989 r_dihedral_angle_3_deg 13.986 r_long_range_B_refined 7.165 r_long_range_B_other 7.164 r_dihedral_angle_1_deg 6.828 r_scangle_other 5.053 r_scbond_it 3.257 r_scbond_other 3.244 r_mcangle_it 2.874 r_mcangle_other 2.873 r_angle_refined_deg 2.038 r_mcbond_it 1.929 r_mcbond_other 1.925 r_angle_other_deg 0.897 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 1789 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing