☰ Navigation Tabs
Crystal structure of the DNA binding domain of Arabidopsis thaliana Auxin Response Factor 1 (AtARF1) in complex with High Affinity DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LDX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 B10 condition of the Morpheus HT screen: 0.09 M (0.3M Sodium fluoride, 0.3M Sodium bromide, 0.3M Sodium iodide); 0.1 M (Tris (base), BICINE pH8.5); 20% v/v Ethylene glycol; 10 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.95 58.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.304 α = 90 b = 102.784 β = 98.036 c = 127.039 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2015-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.65 47.58 88.1 0.999 15.9 3.4 75146 25.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.651 1.68 0.512
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 4LDX 1.65 47.57 1.35 75141 3634 57 0.173 0.1717 0.1728 0.1991 0.2011 38.6
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 14.0494 f_angle_d 0.9634 f_chiral_restr 0.0552 f_bond_d 0.0079 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5526 Nucleic Acid Atoms 855 Solvent Atoms 648 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement XDS data reduction autoPROC data scaling PHASER phasing