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Caldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 100 mM sodium acetate, pH 4.6, 1.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.01 59.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.674 α = 90 b = 94.571 β = 90 c = 170.855 γ = 90
Symmetry Space Group C 2 2 21
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 6M-F 2016-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.283 SLS X10SA
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 1.85 37.9 99.6 0.074 1 19.8 12.9 58917
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 1.85 1.96 97.9 0.779 0.9 2.66 12.9
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 6FJV 1.85 37.9 55970 2946 99.62 0.17409 0.17269 0.1813 0.20058 0.2065 RANDOM 41.66
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] -0.46 -1.78 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.825 r_dihedral_angle_3_deg 12.349 r_dihedral_angle_4_deg 12.117 r_long_range_B_refined 7.619 r_long_range_B_other 7.443 r_dihedral_angle_1_deg 5.895 r_scangle_other 3.408 r_scbond_it 2.146 r_scbond_other 2.146 r_mcangle_other 2.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.825 r_dihedral_angle_3_deg 12.349 r_dihedral_angle_4_deg 12.117 r_long_range_B_refined 7.619 r_long_range_B_other 7.443 r_dihedral_angle_1_deg 5.895 r_scangle_other 3.408 r_scbond_it 2.146 r_scbond_other 2.146 r_mcangle_other 2.092 r_mcangle_it 2.091 r_angle_refined_deg 1.385 r_mcbond_other 1.373 r_mcbond_it 1.372 r_angle_other_deg 0.724 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 3631 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing