☰ Navigation Tabs
Structural basis of a superoxide dismutase from a tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 18% PEG 6000, 0.1 M MES pH 6.5, 0.2 M Potassium chloride, and TCEP addictive
Crystal Properties Matthews coefficient Solvent content 2.06 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.825 α = 90 b = 105.825 β = 90 c = 76.956 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 PIXEL DECTRIS EIGER X 16M 2018-12-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 45.89 99.6 0.051 0.057 0.026 0.999 18.4 4.6 56839 25.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 0.225 0.256 0.121 0.954 7 4.4
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.101 45.866 55983 2800 99.653 0.183 0.1803 0.2281 0.2233 43.165
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] -0.002 -0.001 -0.002 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.702 r_dihedral_angle_4_deg 16.867 r_dihedral_angle_3_deg 16.084 r_lrange_it 7.775 r_scangle_it 7.227 r_dihedral_angle_1_deg 6.48 r_scbond_it 6.173 r_mcangle_it 5.83 r_mcbond_it 5.168 r_angle_refined_deg 1.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.702 r_dihedral_angle_4_deg 16.867 r_dihedral_angle_3_deg 16.084 r_lrange_it 7.775 r_scangle_it 7.227 r_dihedral_angle_1_deg 6.48 r_scbond_it 6.173 r_mcangle_it 5.83 r_mcbond_it 5.168 r_angle_refined_deg 1.487 r_nbtor_refined 0.321 r_nbd_refined 0.218 r_symmetry_nbd_refined 0.206 r_ncsr_local_group_15 0.185 r_xyhbond_nbd_refined 0.183 r_ncsr_local_group_4 0.175 r_ncsr_local_group_11 0.168 r_ncsr_local_group_14 0.163 r_ncsr_local_group_9 0.162 r_ncsr_local_group_3 0.158 r_ncsr_local_group_5 0.157 r_ncsr_local_group_1 0.155 r_ncsr_local_group_13 0.154 r_ncsr_local_group_8 0.153 r_ncsr_local_group_12 0.15 r_symmetry_xyhbond_nbd_refined 0.149 r_ncsr_local_group_10 0.148 r_ncsr_local_group_7 0.147 r_ncsr_local_group_6 0.142 r_ncsr_local_group_2 0.141 r_metal_ion_refined 0.091 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7210 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing