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Sav-SOD: Chimeric Streptavidin-cSOD as Host for Artificial Metalloenzymes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IRW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20 %w/v PEG 3350 (Precipitant)
0.2 M Na K Phos (Salt)
0.1 M BIS-TRIS prop 7.5 pH (Buffer)
Crystal Properties Matthews coefficient Solvent content 1.93 36.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.525 α = 90 b = 102.525 β = 90 c = 59.077 γ = 90
Symmetry Space Group P 42 21 2
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 2020-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 45.893 100 0.999 18.9 24.4 29784
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 100 0.958
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4IRW 1.8 45.893 29743 1445 99.97 0.181 0.1794 0.1801 0.2182 0.2198 27.668
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] -0.195 -0.195 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.538 r_dihedral_angle_4_deg 14.674 r_dihedral_angle_3_deg 11.408 r_dihedral_angle_1_deg 7.921 r_lrange_it 6.619 r_lrange_other 6.519 r_scangle_other 4.667 r_scangle_it 4.66 r_mcangle_it 3.97 r_mcangle_other 3.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.538 r_dihedral_angle_4_deg 14.674 r_dihedral_angle_3_deg 11.408 r_dihedral_angle_1_deg 7.921 r_lrange_it 6.619 r_lrange_other 6.519 r_scangle_other 4.667 r_scangle_it 4.66 r_mcangle_it 3.97 r_mcangle_other 3.968 r_scbond_it 3.098 r_scbond_other 3.071 r_mcbond_it 2.648 r_mcbond_other 2.645 r_angle_refined_deg 1.973 r_angle_other_deg 1.546 r_symmetry_nbd_refined 0.208 r_nbd_refined 0.201 r_chiral_restr 0.199 r_nbd_other 0.198 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.13 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1839 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing Aimless data scaling