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Crystal structure of the DNA binding domain of human transcription factor ERF in the oxidized form, in complex with double-stranded DNA ACCGGAAGTG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 10% PEG 4000, 0.1M Hepes pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.41 72.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.537 α = 90 b = 128.464 β = 90 c = 174.914 γ = 90
Symmetry Space Group I 2 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 2017-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0 APS 21-ID-D
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 4.5 50 99.5 0.082 17.9 5.7 8678
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 4.5 4.58 0.73
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 7JSA 4.51 36.85 8243 434 99.03 0.2263 0.2243 0.2292 0.2642 0.2507 RANDOM 212.875
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] -3.08 1.2 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.688 r_dihedral_angle_3_deg 18.025 r_dihedral_angle_4_deg 15.548 r_dihedral_angle_1_deg 6.448 r_angle_other_deg 1.213 r_angle_refined_deg 1.087 r_chiral_restr 0.05 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.688 r_dihedral_angle_3_deg 18.025 r_dihedral_angle_4_deg 15.548 r_dihedral_angle_1_deg 6.448 r_angle_other_deg 1.213 r_angle_refined_deg 1.087 r_chiral_restr 0.05 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2888 Nucleic Acid Atoms 1612 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