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Crystal structure of the DNA Binding Domain of arabidopsis thaliana auxin response factor 1, P21 structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LDV pdb entry 4LDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1 4 mg/mL ARF1DBD + 1 l crystallization buffer (100 mM MES 6.5, 20%PEG 5K MME) 7.7.11), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.26 α = 90 b = 83.67 β = 117.61 c = 79.027 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 CCD ADSC QUANTUM 315r 2011-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 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 2.67 70.02 96.6 0.098 6.9 3.8 23332 -3 73.1
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 2.67 2.81 96.2 0.65 2.2 3.7 3391
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 pdb entry 4LDV 2.67 35.94 22140 1173 96.1 0.21885 0.21561 0.2163 0.27945 0.2735 RANDOM 69.443
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] -0.52 1.32 -2.85 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.693 r_dihedral_angle_4_deg 19.709 r_dihedral_angle_3_deg 18.589 r_dihedral_angle_1_deg 6.868 r_long_range_B_refined 5.466 r_long_range_B_other 5.464 r_scangle_other 3.089 r_mcangle_it 2.939 r_mcangle_other 2.939 r_scbond_it 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.693 r_dihedral_angle_4_deg 19.709 r_dihedral_angle_3_deg 18.589 r_dihedral_angle_1_deg 6.868 r_long_range_B_refined 5.466 r_long_range_B_other 5.464 r_scangle_other 3.089 r_mcangle_it 2.939 r_mcangle_other 2.939 r_scbond_it 1.87 r_scbond_other 1.869 r_mcbond_it 1.756 r_mcbond_other 1.755 r_angle_refined_deg 1.481 r_angle_other_deg 0.772 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5104 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 2
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling