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Streptavidin mutant S112R_K121E 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 2.93 58.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.261 α = 90 b = 57.261 β = 90 c = 182.104 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 45.53 99.9 0.158 0.998 16.7 23.2 11556
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 3.472 0.84 1.2 23.1
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 41.688 11399 866 98.718 0.212 0.2086 0.2088 0.2576 0.2573 31.331
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] -0.21 -0.21 0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.896 r_dihedral_angle_4_deg 21.273 r_dihedral_angle_3_deg 11.508 r_dihedral_angle_1_deg 8.548 r_lrange_it 5.929 r_lrange_other 5.888 r_scangle_it 4.62 r_scangle_other 4.52 r_mcangle_it 3.811 r_mcangle_other 3.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.896 r_dihedral_angle_4_deg 21.273 r_dihedral_angle_3_deg 11.508 r_dihedral_angle_1_deg 8.548 r_lrange_it 5.929 r_lrange_other 5.888 r_scangle_it 4.62 r_scangle_other 4.52 r_mcangle_it 3.811 r_mcangle_other 3.809 r_scbond_it 3.368 r_scbond_other 3.241 r_mcbond_other 2.968 r_mcbond_it 2.967 r_angle_other_deg 2.56 r_angle_refined_deg 1.925 r_symmetry_nbd_other 0.222 r_nbd_other 0.211 r_nbd_refined 0.191 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.134 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.079 r_bond_other_d 0.038 r_gen_planes_other 0.015 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 901 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing