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Crystal structure of the core streptavidin mutant V212 (Y22S/N23D/S27D/S45N/Y83S/R84K/E101D/R103K/E116N) complexed with bis iminobiotin long tail (Bis-IMNtail) at 1.3 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 7.4 293 0.2 M sodium fluoride, 20% PEG3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.354 α = 90 b = 77.377 β = 90 c = 174.122 γ = 90
Symmetry Space Group C 2 2 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 RAYONIX MX300HE 2013-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 1.3 50 99.6 0.056 35.8 8 127717 127145
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 1.3 1.35 99.6 0.358 3.86 8 127717
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 1.3 50 120725 6384 99.54 0.14778 0.14565 0.1805 0.18787 0.2146 RANDOM 22.869
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] 0.91 0.54 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.41 r_dihedral_angle_4_deg 27.757 r_sphericity_free 26.955 r_dihedral_angle_3_deg 13.838 r_sphericity_bonded 13.462 r_dihedral_angle_1_deg 6.888 r_long_range_B_refined 6.048 r_long_range_B_other 5.993 r_mcangle_other 5.746 r_mcangle_it 5.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.41 r_dihedral_angle_4_deg 27.757 r_sphericity_free 26.955 r_dihedral_angle_3_deg 13.838 r_sphericity_bonded 13.462 r_dihedral_angle_1_deg 6.888 r_long_range_B_refined 6.048 r_long_range_B_other 5.993 r_mcangle_other 5.746 r_mcangle_it 5.726 r_scangle_other 5.524 r_rigid_bond_restr 5.425 r_mcbond_it 4.715 r_scbond_it 4.687 r_scbond_other 4.685 r_mcbond_other 4.659 r_angle_refined_deg 2.23 r_angle_other_deg 1.05 r_chiral_restr 0.379 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 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 3624 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 100
Software Software Software Name Purpose BSS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling