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Crystal structure of the core streptavidin mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) complexed with iminobiotin long tail (IMNtail) at 1.2 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 7.5 293 0.2 M sodium citrate tribasic dehydrate, 0.1 M HEPES sodium, 35%(w/v) (+/-)-2-methyl-2, 4-pentandiol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.969 α = 90 b = 57.5 β = 103.34 c = 71.807 γ = 90
Symmetry Space Group P 1 21 1
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 MX225HE 2012-10-16 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 1.2 50 96.6 0.068 18.3 3.5 148314 143314
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 1.2 1.24 96.6 0.309 2.75 3.5 148314
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 1.2 15 135778 7184 96.49 0.13487 0.1335 0.1421 0.16056 0.1655 RANDOM 11.669
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] 0.07 0.1 -0.15 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.15 r_dihedral_angle_3_deg 11.262 r_dihedral_angle_4_deg 10.244 r_dihedral_angle_1_deg 7.12 r_scangle_it 6.592 r_scbond_it 5.039 r_mcangle_it 4.224 r_mcbond_it 2.97 r_rigid_bond_restr 2.749 r_angle_refined_deg 2.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.15 r_dihedral_angle_3_deg 11.262 r_dihedral_angle_4_deg 10.244 r_dihedral_angle_1_deg 7.12 r_scangle_it 6.592 r_scbond_it 5.039 r_mcangle_it 4.224 r_mcbond_it 2.97 r_rigid_bond_restr 2.749 r_angle_refined_deg 2.272 r_chiral_restr 0.323 r_bond_refined_d 0.026 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3594 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 126
Software Software Software Name Purpose BSS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling