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Crystal structure of actinomycin D-echinomycin-d(AGCCCGT/ACGGGCT) complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.25 mM Oligonucleotides, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate (pH 6.5), 0.5 mM Spermine tetrahydrochloride, 6 mM Zinc chloride, 3.5 mM Potassium chloride, PEG200 3% (v/v), Reservoir PEG 200 (30% v/v)
Crystal Properties Matthews coefficient Solvent content 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.452 α = 90 b = 43.452 β = 90 c = 139.365 γ = 120
Symmetry Space Group P 63 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 2019-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 30 97.8 0.057 0.06 0.018 7.7 12.3 7161 19.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 93.1 0.399 0.034 0.01 0.999 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7DQ0 1.95 25.57 1.36 7161 701 66.6 0.234 0.229 0.2309 0.282 0.2766 25.47
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 143 Nucleic Acid Atoms 287 Solvent Atoms 26 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing