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Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 294 1.6 M ammonium sulphate, 0.1 M sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 4.12 70.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.845 α = 90 b = 191.845 β = 90 c = 87.556 γ = 120
Symmetry Space Group P 61 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 CCD RAYONIX MX300-HS 2015-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 3.1 50 99.8 0.11 19 5.9 17757 2
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 5E8I 3.1 40 16790 885 99.68 0.19629 0.19414 0.196 0.23716 0.2317 RANDOM
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] -0.92 -0.46 -0.92 3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.536 r_dihedral_angle_4_deg 18.456 r_dihedral_angle_3_deg 16.548 r_dihedral_angle_1_deg 5.905 r_long_range_B_refined 3.719 r_long_range_B_other 3.714 r_mcangle_it 2.292 r_mcangle_other 2.292 r_scangle_other 1.808 r_mcbond_it 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.536 r_dihedral_angle_4_deg 18.456 r_dihedral_angle_3_deg 16.548 r_dihedral_angle_1_deg 5.905 r_long_range_B_refined 3.719 r_long_range_B_other 3.714 r_mcangle_it 2.292 r_mcangle_other 2.292 r_scangle_other 1.808 r_mcbond_it 1.27 r_mcbond_other 1.27 r_angle_other_deg 1.141 r_angle_refined_deg 1.128 r_scbond_it 1.023 r_scbond_other 0.992 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_bond_other_d 0.006 r_gen_planes_refined 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2334 Nucleic Acid Atoms 1330 Solvent Atoms 2 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing