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Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with biotin long tail (BTNtail) at 1.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WYQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.1 M cadmium chloride hydrate, 0.1 M sodium acetate trihydrate, 30%(v/v) PEG400, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.92 35.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.241 α = 90 b = 85.461 β = 90 c = 86.115 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2012-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98000 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.5 50 97.4 0.035 17.6 6.3 65724 64012
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 97.4 0.232 3.08 6.3 64012
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WYQ 1.5 50 60475 3235 96.94 0.17613 0.1729 0.1769 0.23616 0.2413 RANDOM 15.935
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] -0.4 1.66 -1.26
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.256 r_dihedral_angle_2_deg 26.406 r_dihedral_angle_3_deg 14.443 r_dihedral_angle_4_deg 12.47 r_sphericity_bonded 10.738 r_dihedral_angle_1_deg 7.272 r_scangle_other 5.436 r_long_range_B_other 5.177 r_long_range_B_refined 5.176 r_scbond_other 4.779
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.256 r_dihedral_angle_2_deg 26.406 r_dihedral_angle_3_deg 14.443 r_dihedral_angle_4_deg 12.47 r_sphericity_bonded 10.738 r_dihedral_angle_1_deg 7.272 r_scangle_other 5.436 r_long_range_B_other 5.177 r_long_range_B_refined 5.176 r_scbond_other 4.779 r_scbond_it 4.778 r_rigid_bond_restr 3.63 r_mcangle_other 3.619 r_mcangle_it 3.618 r_mcbond_it 2.999 r_mcbond_other 2.952 r_angle_refined_deg 1.912 r_angle_other_deg 0.877 r_chiral_restr 0.135 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3652 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 159
Software Software Software Name Purpose SERGUI data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling