☰ Navigation Tabs
Structure of the Clr-cAMP-DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 281 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-butanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG3350, 0.44 mM Clr, 25 mM cGMP, 25 mM magnesium chloride, 0.55 mM dsDNA
Crystal Properties Matthews coefficient Solvent content 2.48 50.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.71 α = 90 b = 72.9 β = 90 c = 199.99 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 PIXEL DECTRIS EIGER X 16M 2019-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 3.12 49.15 70.19 0.056 0.064 1 11.08 4.3 9719 100.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.12 3.23 5.53 0.481 0.621 0.61 1.87 2
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 FREE R-VALUE 4CYD 3.12 49.2 1.36 9716 469 69.93 0.2914 0.2894 0.287 0.3331 0.3273 98.23
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 24.7557 f_angle_d 1.0821 f_chiral_restr 0.0583 f_plane_restr 0.0136 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3466 Nucleic Acid Atoms 1161 Solvent Atoms 3 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing