☰ Navigation Tabs
Crystal structure of ALiS4-Streptavidin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y59
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M Tris-HCl (pH8.0), 30%(w/v) PEG 1000, 2.0% agarose hydrogel
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.921 α = 90 b = 84.423 β = 98.98 c = 46.138 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 2015-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 57.21 94.5 0.058 12.8 3.2 66421
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 87.8 0.352 1.9 2.3
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 4Y59 1.5 57.21 63027 3384 94.18 0.14731 0.14484 0.1459 0.19307 0.1938 RANDOM 17.324
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] -0.77 -0.04 0.57 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.352 r_dihedral_angle_4_deg 21.743 r_sphericity_free 19.343 r_dihedral_angle_3_deg 12.874 r_sphericity_bonded 8.085 r_dihedral_angle_1_deg 7.063 r_rigid_bond_restr 5.849 r_scangle_other 3.626 r_long_range_B_refined 3.619 r_long_range_B_other 3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.352 r_dihedral_angle_4_deg 21.743 r_sphericity_free 19.343 r_dihedral_angle_3_deg 12.874 r_sphericity_bonded 8.085 r_dihedral_angle_1_deg 7.063 r_rigid_bond_restr 5.849 r_scangle_other 3.626 r_long_range_B_refined 3.619 r_long_range_B_other 3.5 r_scbond_it 3.261 r_scbond_other 3.261 r_mcangle_other 3.051 r_mcangle_it 3.05 r_mcbond_it 2.629 r_mcbond_other 2.623 r_angle_refined_deg 1.868 r_angle_other_deg 0.871 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3592 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing