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Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with 16-mer DNA CAGAGGATGTGGCTTC
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 294 1.6 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.59 65.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.422 α = 90 b = 90.732 β = 90 c = 165.204 γ = 90
Symmetry Space Group I 21 21 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 MX300-HS 2017-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 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 3.65 50 95.8 0.122 8.1 5.2 6615 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 3.65 3.71 0.493
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 5JVT 3.9 35 5326 260 97.71 0.2495 0.2474 0.253 0.2943 0.3082 RANDOM 125.421
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] -11.96 24.57 -12.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.013 r_dihedral_angle_4_deg 20.109 r_dihedral_angle_3_deg 18.404 r_dihedral_angle_1_deg 5.922 r_angle_other_deg 1.544 r_angle_refined_deg 1.063 r_chiral_restr 0.057 r_bond_other_d 0.015 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.013 r_dihedral_angle_4_deg 20.109 r_dihedral_angle_3_deg 18.404 r_dihedral_angle_1_deg 5.922 r_angle_other_deg 1.544 r_angle_refined_deg 1.063 r_chiral_restr 0.057 r_bond_other_d 0.015 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1525 Nucleic Acid Atoms 1299 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing