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Crystal structure of the DNA binding domain of A. thailana auxin response factor 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMet derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 0.75 l of 4mg/mL ARF1DBD + 0.75 l crystallization buffer (2.9 M NaFormate, 0.1 M MES 6.0, 50 mM KI), pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.362 α = 90 b = 126.256 β = 90 c = 83.672 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 315r 2011-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97625 ESRF ID14-4
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 1.45 39.08 98.9 0.093 7.3 3.2 81768 -3 18.4
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 1.45 1.53 99.9 0.58 1.4 2.7 11957
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SeMet derivative 1.45 39.08 77670 4079 97.15 0.21101 0.2093 0.2075 0.24344 0.242 RANDOM 18.723
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] 0.25 -0.61 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.299 r_dihedral_angle_4_deg 17.244 r_dihedral_angle_3_deg 13.354 r_long_range_B_refined 6.954 r_dihedral_angle_1_deg 6.054 r_mcangle_it 2.394 r_scbond_it 1.716 r_angle_refined_deg 1.565 r_mcbond_it 1.413 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.299 r_dihedral_angle_4_deg 17.244 r_dihedral_angle_3_deg 13.354 r_long_range_B_refined 6.954 r_dihedral_angle_1_deg 6.054 r_mcangle_it 2.394 r_scbond_it 1.716 r_angle_refined_deg 1.565 r_mcbond_it 1.413 r_chiral_restr 0.11 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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 2591 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 23
Software Software Software Name Purpose MxCuBE data collection REFMAC refinement MOSFLM data reduction SCALA data scaling