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Structure of the DNA binding ETS domain of human ETV4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BNC PDB ENTRY 4BNC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.8 M SODIUM CITRATE TRIBASIC, 0.1 M CACODYLATE PH 6.5.
Crystal Properties Matthews coefficient Solvent content 1.61 23.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.801 α = 90 b = 50.801 β = 90 c = 67.66 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS PILATUS 6M 2014-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.05 26.8 96.5 0.04 21.1 8.8 46056 -3
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 1.05 1.07 67.5 0.67 2.1 4.7
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 4BNC 1.05 43.99 43771 2245 96.46 0.11727 0.11654 0.1318 0.13201 0.144 RANDOM 15.559
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] 0.22 0.11 0.22 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.056 r_sphericity_free 32.534 r_dihedral_angle_4_deg 19.917 r_dihedral_angle_3_deg 12.117 r_sphericity_bonded 8.663 r_dihedral_angle_1_deg 5.462 r_long_range_B_refined 3.545 r_long_range_B_other 3.544 r_scangle_other 2.257 r_mcangle_other 1.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.056 r_sphericity_free 32.534 r_dihedral_angle_4_deg 19.917 r_dihedral_angle_3_deg 12.117 r_sphericity_bonded 8.663 r_dihedral_angle_1_deg 5.462 r_long_range_B_refined 3.545 r_long_range_B_other 3.544 r_scangle_other 2.257 r_mcangle_other 1.933 r_mcangle_it 1.927 r_scbond_it 1.806 r_scbond_other 1.793 r_angle_refined_deg 1.348 r_rigid_bond_restr 1.34 r_mcbond_it 1.323 r_mcbond_other 1.321 r_angle_other_deg 0.814 r_chiral_restr 0.089 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 800 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing