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Streptavidin mutant S112R with a biotC4-1 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 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.146 α = 90 b = 57.146 β = 90 c = 182.564 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 1.0000 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 1.95 45.69 100 0.102 0.999 23.2 24.1 11549
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 2 100 1.9 0.907 26
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 1.95 45.64 11469 576 99.419 0.193 0.1914 0.1914 0.2305 0.2324 37.149
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] 0.39 0.39 -0.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.069 r_dihedral_angle_4_deg 23.088 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 8.286 r_lrange_other 7.343 r_lrange_it 7.299 r_scangle_other 5.624 r_scangle_it 5.513 r_mcangle_it 4.345 r_mcangle_other 4.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.069 r_dihedral_angle_4_deg 23.088 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 8.286 r_lrange_other 7.343 r_lrange_it 7.299 r_scangle_other 5.624 r_scangle_it 5.513 r_mcangle_it 4.345 r_mcangle_other 4.342 r_scbond_other 3.944 r_scbond_it 3.912 r_mcbond_it 3.33 r_mcbond_other 3.328 r_angle_other_deg 2.548 r_angle_refined_deg 1.858 r_nbd_other 0.264 r_symmetry_nbd_other 0.232 r_nbd_refined 0.216 r_symmetry_nbd_refined 0.197 r_symmetry_xyhbond_nbd_refined 0.196 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.123 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.075 r_bond_other_d 0.038 r_gen_planes_other 0.015 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 923 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing