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Crystal structure of the DNA binding domain of the G245A mutant of arabidopsis thaliana auxin reponse factor 1
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 7 293 0.75 l of 13 mg/ml Arf1dbd-g245a +0.75 l crystallization buffer (100 mM bis-tris-propane pH 7.0, 0.7 M succinic acid), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.69 54.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.1 α = 90 b = 84.24 β = 114.76 c = 78.96 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 PSI PILATUS 6M 2012-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9795 ALBA XALOC
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 2.3 71.7 99.9 0.102 5.9 3.1 38764 -3 41.1
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 2.3 2.42 100 0.63 1.8 3.2 5641
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 2.3 63.91 36804 1943 99.87 0.21263 0.21015 0.2128 0.2588 0.2585 RANDOM 60.556
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] -0.83 1.33 -0.58 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.148 r_dihedral_angle_4_deg 17.695 r_dihedral_angle_3_deg 17.289 r_dihedral_angle_1_deg 7.532 r_long_range_B_refined 7.115 r_long_range_B_other 7.104 r_scangle_other 4.215 r_mcangle_it 3.83 r_mcangle_other 3.83 r_scbond_it 2.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.148 r_dihedral_angle_4_deg 17.695 r_dihedral_angle_3_deg 17.289 r_dihedral_angle_1_deg 7.532 r_long_range_B_refined 7.115 r_long_range_B_other 7.104 r_scangle_other 4.215 r_mcangle_it 3.83 r_mcangle_other 3.83 r_scbond_it 2.604 r_scbond_other 2.604 r_mcbond_it 2.368 r_mcbond_other 2.368 r_angle_refined_deg 1.641 r_angle_other_deg 0.799 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 5239 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling