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Structure of indole-3-acetic acid-amido synthetase GH3.6 from A.thaliana in complex with AMP and aspartate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KOD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 Starting drop: 100 mM MES, pH 6.5, 0.6 M NaCl, 18% PEG 4000, 10 mM AMP and 1 mM Asp; protein: AtGH3.6 at 7.1 mg/ml in 20 mM HEPES pH 7.5, 100 mM NaCl, 1 mM MgCl2 and 1% glycerol
Crystal Properties Matthews coefficient Solvent content 2.77 55.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.886 α = 90 b = 197.886 β = 90 c = 65.284 γ = 120
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 DECTRIS EIGER X 16M 2023-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.987 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.736 98.943 96 0.1607 0.1663 0.0425 0.999 11.26 15.22 96838
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.736 1.967 70.3 1.4285 1.49 0.4209 0.705 1.88 12.28 4844
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 1.736 25.3 96781 4781 64.3 0.1988 0.1976 0.1874 0.2215 0.2123 RANDOM 33.44
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] 0.8542 0.8542 -1.7083
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.73 t_omega_torsion 3.83 t_angle_deg 1.06 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9280 Nucleic Acid Atoms Solvent Atoms 676 Heterogen Atoms 64
Software Software Software Name Purpose MxCuBE data collection BUSTER refinement autoPROC data processing STARANISO data scaling Aimless data scaling autoPROC data reduction PHASER phasing Coot model building XDS data reduction