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CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 297 0.2 M AMMONIUM ACETATE, 0.15 M MAGNESIUM ACETATE, 5% W/V PEG 4000, 50 MM HEPES BUFFER, PH 7.0 AT 24 DEGREES C
Crystal Properties Matthews coefficient Solvent content 3.28 61.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.094 α = 90 b = 104.073 β = 90 c = 116.185 γ = 90
Symmetry Space Group P 21 21 21
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 RAXIS4 MIRRORS 2000-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU SPring-8 BL45XU
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 2.65 20 94.5 0.047 26.6 3.436 17550 40.9
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 2.65 2.7 88.9 0.092 10.9 2.91
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 1IO4 2.65 18.01 17550 876 94.5 0.223 0.223 0.2151 0.263 RANDOM 52.4
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] -25.93 -21.77 47.69
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_scangle_it 8.14 c_mcangle_it 6.55 c_scbond_it 5.89 c_mcbond_it 4.43 c_angle_deg 1.4 c_improper_angle_d 1.13 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_scangle_it 8.14 c_mcangle_it 6.55 c_scbond_it 5.89 c_mcbond_it 4.43 c_angle_deg 1.4 c_improper_angle_d 1.13 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1826 Nucleic Acid Atoms 1300 Solvent Atoms 58 Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing