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R164N mutant of the RUNX1 Runt domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EAO PDB ENTRY 1EAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 22% PEG 8000, 0.1M SODIUM CACODYLATE PH=6.5, 0.2M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.948 α = 90 b = 46.497 β = 90.66 c = 63.552 γ = 90
Symmetry Space Group C 1 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 CCD BUILT IN ANL 2005-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-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 2.6 50 94.5 0.12 19.6 4.5 7962 2
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 2.6 2.64 73.9 0.39 2.3 2.6
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EAO 2.6 50 7186 776 94.6 0.214 0.209 0.213 0.268 RANDOM 46.44
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] 0.71 -1.01 -1.95 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.479 r_dihedral_angle_3_deg 10.071 r_dihedral_angle_4_deg 9.051 r_dihedral_angle_1_deg 2.769 r_angle_refined_deg 2.238 r_angle_other_deg 1.774 r_scangle_it 0.215 r_scbond_it 0.13 r_nbtor_refined 0.125 r_nbd_refined 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.479 r_dihedral_angle_3_deg 10.071 r_dihedral_angle_4_deg 9.051 r_dihedral_angle_1_deg 2.769 r_angle_refined_deg 2.238 r_angle_other_deg 1.774 r_scangle_it 0.215 r_scbond_it 0.13 r_nbtor_refined 0.125 r_nbd_refined 0.118 r_mcangle_it 0.095 r_nbd_other 0.094 r_symmetry_vdw_other 0.081 r_mcbond_it 0.081 r_xyhbond_nbd_refined 0.068 r_nbtor_other 0.06 r_symmetry_hbond_refined 0.058 r_chiral_restr 0.045 r_symmetry_vdw_refined 0.041 r_bond_refined_d 0.022 r_bond_other_d 0.005 r_gen_planes_refined 0.001 r_gen_planes_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 1894 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL data reduction SCALEPACK data scaling AMoRE phasing