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The crystal structures of the DNA binding sites of the RUNX1 transcription factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other FIBER A-DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 MPD, magnesium chloride, sodium cacodylate acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.83 32.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.032 α = 90 b = 41.032 β = 90 c = 23.8 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ OSMIC CONFOCAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 18.4 95.9 0.039 39.3 3.3 4315
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.73 78.4 0.236 4.9 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FIBER A-DNA 1.7 15 4227 210 89.7 0.1658 0.1658 0.1617 0.1632 0.2506 0.2136 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 432
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.091 s_angle_d 0.025 s_similar_dist 0.025 s_bond_d 0.008 s_anti_bump_dis_restr 0.007 s_non_zero_chiral_vol 0.006 s_from_restr_planes 0.0007 s_zero_chiral_vol s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 330 Solvent Atoms 102 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling ULTIMA model building SHELXL-97 refinement ULTIMA phasing