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Streptavidin with a fluorescent substrate
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 4 298 2.0 M ammonium sulfate, 0.1 M sodium acetate
26 mg/ml protein
Crystal Properties Matthews coefficient Solvent content 2.33 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.71 α = 90 b = 57.71 β = 90 c = 183.617 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 2021-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999998 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.546 45.9 95.2 0.092 0.095 0.026 0.999 20.6 20 22167
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.57 2.466 2.643 0.916 0.425 14.9
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 1.546 42.024 22140 1091 94.989 0.177 0.176 0.1755 0.1993 0.1957 29.613
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] -1.239 -1.239 2.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.852 r_dihedral_angle_6_deg 16.643 r_dihedral_angle_3_deg 11.916 r_dihedral_angle_1_deg 7.919 r_lrange_it 7.115 r_lrange_other 7.105 r_scangle_other 5.927 r_scangle_it 5.924 r_mcangle_other 4.349 r_mcangle_it 4.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.852 r_dihedral_angle_6_deg 16.643 r_dihedral_angle_3_deg 11.916 r_dihedral_angle_1_deg 7.919 r_lrange_it 7.115 r_lrange_other 7.105 r_scangle_other 5.927 r_scangle_it 5.924 r_mcangle_other 4.349 r_mcangle_it 4.347 r_scbond_it 3.957 r_scbond_other 3.954 r_mcbond_it 2.926 r_mcbond_other 2.906 r_angle_refined_deg 1.589 r_angle_other_deg 0.584 r_symmetry_nbd_refined 0.217 r_symmetry_nbd_other 0.2 r_nbd_refined 0.193 r_nbtor_refined 0.182 r_nbd_other 0.171 r_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_refined 0.108 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.083 r_chiral_restr_other 0.033 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 931 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing Aimless data scaling PDB_EXTRACT data extraction Coot model building