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Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0
Crystal Properties Matthews coefficient Solvent content 4.03 69.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.917 α = 90 b = 103.917 β = 90 c = 322.912 γ = 120
Symmetry Space Group P 62 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 2016-10-22 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 4.25 50 94.7 0.103 17.9 6.1 7550
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.25 4.32 1.382 0.785
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 6VGD 4.25 35 7120 408 95.03 0.3128 0.3125 0.3137 0.3172 0.321 RANDOM 282.708
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 1.54 3.08 -10.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.371 r_dihedral_angle_4_deg 16.804 r_dihedral_angle_3_deg 16.724 r_dihedral_angle_1_deg 6.838 r_angle_refined_deg 1.177 r_angle_other_deg 1.108 r_chiral_restr 0.044 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.371 r_dihedral_angle_4_deg 16.804 r_dihedral_angle_3_deg 16.724 r_dihedral_angle_1_deg 6.838 r_angle_refined_deg 1.177 r_angle_other_deg 1.108 r_chiral_restr 0.044 r_bond_refined_d 0.003 r_gen_planes_refined 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 2705 Nucleic Acid Atoms 656 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