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Crystal structure of Amborella trichopoda ACCO2 in complex with Fe and ACC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 298 20 mM Xylitol, 20 mM Myo-Inositol, 20 mM D-(-)Fructose, 20 mM L-Rhamnose monohydrate, 20 uM D-Sorbitol;
100 mM BES, Triethanolamine (TEA), pH 7.5;
31% w/v Percipitant Mix 8 (10% w/v PEG 20000, 50% w/v Trimethylpropane, 2% w/v NDSB 195)
Crystal Properties Matthews coefficient Solvent content 2 38.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.278 α = 90 b = 58.777 β = 90 c = 112.724 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER2 XE 16M 2024-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.94054 Diamond I03
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 1.65 52.1 100 0.1 0.105 0.031 0.999 11 10.7 35463 21.04
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 1.65 1.68 100 1.092 1.146 0.343 0.805 1.7 10.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 40.68 1.34 35373 1760 99.81 0.1776 0.1762 0.1777 0.2037 0.205 28.76
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.908 f_angle_d 1.1087 f_chiral_restr 0.0758 f_bond_d 0.0114 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2480 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing