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THE RUNX1 Runt domain at 1.70A resolution: A structural switch and specifically bound chloride ions modulate DNA binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EAQ PDB CODE 1EAQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 30% MPEG 350, 5-10% PEG 3350, 70 MM NA CACODYLATE, PH 6.5
Crystal Properties Matthews coefficient Solvent content 4.46 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.696 α = 90 b = 110.696 β = 90 c = 117.293 γ = 120
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 ADSC CCD MIRROR 1999-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.7 19.7 99.7 0.04 11.3 5.7 28866
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 1.7 1.74 99 0.58 1.5 4
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB CODE 1EAQ 1.7 20 28868 1519 99.7 0.204 0.222 0.267 RANDOM 21.44
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] 1.56 0.78 1.56 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.478 r_dihedral_angle_1_deg 5.017 r_scangle_it 1.854 r_angle_refined_deg 1.586 r_angle_other_deg 1.501 r_scbond_it 1.13 r_symmetry_hbond_refined 0.812 r_mcangle_it 0.809 r_mcbond_it 0.433 r_symmetry_vdw_other 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.478 r_dihedral_angle_1_deg 5.017 r_scangle_it 1.854 r_angle_refined_deg 1.586 r_angle_other_deg 1.501 r_scbond_it 1.13 r_symmetry_hbond_refined 0.812 r_mcangle_it 0.809 r_mcbond_it 0.433 r_symmetry_vdw_other 0.217 r_nbd_refined 0.206 r_nbd_other 0.204 r_xyhbond_nbd_refined 0.141 r_symmetry_vdw_refined 0.113 r_chiral_restr 0.103 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_bond_refined_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 875 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing