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Crystal structure of the DNA binding domain of FLI1 (wild-type) in complex with a DNA containing two contiguous GGAA sites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 0.1 M Tris, pH 8.5, 2 M ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 2.55 51.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.949 α = 90 b = 96.949 β = 90 c = 185.748 γ = 90
Symmetry Space Group I 41 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 PIXEL DECTRIS EIGER X 16M 2020-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.59 50 98.9 0.071 1 47 13.6 13984 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.63 0.899
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 PDB entry 5JVT 2.59 40 13295 674 98.82 0.26179 0.26048 0.2645 0.28738 0.2916 RANDOM 98.744
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] -1.71 -1.71 3.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.723 r_dihedral_angle_3_deg 21.16 r_dihedral_angle_4_deg 17.639 r_long_range_B_refined 8.436 r_long_range_B_other 8.434 r_dihedral_angle_1_deg 7.549 r_mcangle_it 5.399 r_mcangle_other 5.396 r_scangle_other 4.286 r_mcbond_other 3.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.723 r_dihedral_angle_3_deg 21.16 r_dihedral_angle_4_deg 17.639 r_long_range_B_refined 8.436 r_long_range_B_other 8.434 r_dihedral_angle_1_deg 7.549 r_mcangle_it 5.399 r_mcangle_other 5.396 r_scangle_other 4.286 r_mcbond_other 3.188 r_mcbond_it 3.186 r_scbond_other 2.476 r_scbond_it 2.475 r_angle_refined_deg 1.376 r_angle_other_deg 1.293 r_chiral_restr 0.062 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.003 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 1531 Nucleic Acid Atoms 608 Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing