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Streptavidin wildtype 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 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.714 α = 90 b = 57.714 β = 90 c = 184.135 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 1.55 46.076 100 0.069 1 28.8 25.3 23212
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 1.55 1.58 100 1.704 0.793
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 1.55 46.076 23178 1161 99.931 0.17 0.1688 0.1687 0.2004 0.2003 23.969
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] -0.3 -0.3 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.226 r_dihedral_angle_4_deg 23.562 r_dihedral_angle_3_deg 10.954 r_dihedral_angle_1_deg 7.367 r_lrange_it 6.558 r_lrange_other 6.531 r_scangle_it 4.764 r_scangle_other 4.761 r_scbond_it 3.308 r_scbond_other 3.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.226 r_dihedral_angle_4_deg 23.562 r_dihedral_angle_3_deg 10.954 r_dihedral_angle_1_deg 7.367 r_lrange_it 6.558 r_lrange_other 6.531 r_scangle_it 4.764 r_scangle_other 4.761 r_scbond_it 3.308 r_scbond_other 3.305 r_mcangle_other 3.254 r_mcangle_it 3.248 r_angle_other_deg 2.514 r_mcbond_it 2.291 r_mcbond_other 2.188 r_angle_refined_deg 2.165 r_symmetry_nbd_refined 0.38 r_nbd_other 0.239 r_symmetry_nbd_other 0.231 r_nbd_refined 0.208 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_refined 0.099 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.084 r_bond_other_d 0.038 r_gen_planes_other 0.023 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 904 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing