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Streptavidin mutant S112R with a biotC5-1 cofactor - an artificial iron hydroxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 2 M (NH4)2SO4, 0.1 M Na-Acetate, pH 4
Crystal Properties Matthews coefficient Solvent content 2.29 46.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.633 α = 90 b = 57.633 β = 90 c = 183.649 γ = 90
Symmetry Space Group I 41 2 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 2019-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 1.49 45.91 99.6 0.094 1 19.3 24.9 25967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.51 92.7 2.7 1.2 23
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 FREE R-VALUE 3PK2 1.49 45.91 25938 1284 99.524 0.17 0.1688 0.1686 0.1916 0.1898 21.79
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] 0.078 0.078 -0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.414 r_dihedral_angle_4_deg 12.269 r_dihedral_angle_3_deg 9.714 r_dihedral_angle_1_deg 7.31 r_lrange_it 6.029 r_lrange_other 6.013 r_scangle_it 4.844 r_scangle_other 4.84 r_scbond_it 3.276 r_scbond_other 3.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.414 r_dihedral_angle_4_deg 12.269 r_dihedral_angle_3_deg 9.714 r_dihedral_angle_1_deg 7.31 r_lrange_it 6.029 r_lrange_other 6.013 r_scangle_it 4.844 r_scangle_other 4.84 r_scbond_it 3.276 r_scbond_other 3.272 r_mcangle_other 3.235 r_mcangle_it 3.233 r_angle_other_deg 2.527 r_mcbond_it 2.156 r_mcbond_other 2.095 r_angle_refined_deg 1.979 r_symmetry_nbd_other 0.223 r_nbd_other 0.216 r_nbtor_refined 0.177 r_nbd_refined 0.174 r_symmetry_nbd_refined 0.167 r_xyhbond_nbd_refined 0.127 r_symmetry_xyhbond_nbd_refined 0.121 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.084 r_bond_other_d 0.038 r_gen_planes_other 0.018 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 924 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing