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Caldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex, zinc soak
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FNN
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 59.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.164 α = 90 b = 94.832 β = 90 c = 171.013 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 2016-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 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 1.95 37.8 99.7 0.081 1 14.4 6.9 50327
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 1.95 2.06 98.3 1.03 0.759 1.7 6.88
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 6FNN 1.95 37.8 47811 2516 99.69 0.17795 0.17673 0.1853 0.20085 0.2108 RANDOM 44.397
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] -0.89 -2.27 3.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.762 r_dihedral_angle_3_deg 12.572 r_dihedral_angle_4_deg 12.327 r_long_range_B_refined 7.641 r_long_range_B_other 7.545 r_dihedral_angle_1_deg 5.696 r_scangle_other 3.183 r_mcangle_other 2.288 r_mcangle_it 2.287 r_scbond_it 2.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.762 r_dihedral_angle_3_deg 12.572 r_dihedral_angle_4_deg 12.327 r_long_range_B_refined 7.641 r_long_range_B_other 7.545 r_dihedral_angle_1_deg 5.696 r_scangle_other 3.183 r_mcangle_other 2.288 r_mcangle_it 2.287 r_scbond_it 2.039 r_scbond_other 2.038 r_mcbond_it 1.475 r_mcbond_other 1.471 r_angle_refined_deg 1.313 r_angle_other_deg 0.701 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 3572 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing