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Crystal structure of the DNA binding domain of Arabidopsis thaliana auxin response factor 5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100 nL 13 mg/mL ARF5DBD +100 nl crystallization buffer (20 mM TRIS 7.5, 12.5% PEG MME 2000), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.613 α = 90 b = 91.502 β = 114.28 c = 77.182 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 210 2010-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93340 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.15 45 99.8 0.063 11 2.8 23983 -3 30.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.27 100 0.43 2.9 2.8 3492
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.15 38.38 22772 1211 99.69 0.19771 0.19475 0.1984 0.25206 0.2532 RANDOM 26.435
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] -2.43 -0.46 -2.39 3.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.58 r_dihedral_angle_4_deg 24.08 r_dihedral_angle_3_deg 17.921 r_dihedral_angle_1_deg 7 r_long_range_B_refined 6.686 r_mcangle_it 2.737 r_scbond_it 2.047 r_mcbond_it 1.748 r_angle_refined_deg 1.626 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.58 r_dihedral_angle_4_deg 24.08 r_dihedral_angle_3_deg 17.921 r_dihedral_angle_1_deg 7 r_long_range_B_refined 6.686 r_mcangle_it 2.737 r_scbond_it 2.047 r_mcbond_it 1.748 r_angle_refined_deg 1.626 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2651 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 2
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling