☰ Navigation Tabs
Crystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor 1 (ARF1) in complex with protomor-like sequence ER7
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 8.5 293 100 nL complex (4 mg/mL ARF1) and 100 nL crystallization buffer (10% PEG 20K, Glycine pH 8.5, 7.5% propanediol), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.04 59.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.52 α = 90 b = 105.19 β = 98.14 c = 127.91 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 210 2011-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 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 2.9 35 98.7 0.16 6.2 2.6 25033 -3 55
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 2.9 3.06 98.8 0.634 1.7 2.6 3622
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 2.9 33.81 23815 1203 98.41 0.21626 0.21413 0.2183 0.25932 0.2633 RANDOM 47.427
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] -2.58 1.21 3.16 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.633 r_dihedral_angle_3_deg 19.479 r_dihedral_angle_4_deg 16.783 r_dihedral_angle_1_deg 6.969 r_long_range_B_refined 5.949 r_long_range_B_other 5.948 r_mcangle_it 3.918 r_mcangle_other 3.917 r_scangle_other 3.271 r_mcbond_it 2.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.633 r_dihedral_angle_3_deg 19.479 r_dihedral_angle_4_deg 16.783 r_dihedral_angle_1_deg 6.969 r_long_range_B_refined 5.949 r_long_range_B_other 5.948 r_mcangle_it 3.918 r_mcangle_other 3.917 r_scangle_other 3.271 r_mcbond_it 2.246 r_mcbond_other 2.245 r_scbond_it 1.892 r_scbond_other 1.892 r_angle_refined_deg 1.502 r_angle_other_deg 1.146 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 5386 Nucleic Acid Atoms 855 Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection REFMAC refinement MOSFLM data reduction SCALA data scaling