☰ Navigation Tabs
Crystal structure of Amborella trichopoda ACCO2 mutant - Y163F 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 0.09 M Halogens (0.3M Magnesium chloride hexahydrate; 0.3M calcium chloride dihydrate)
0.1M Buffer System 2 (1.0M Sodium HEPES/MOPS(acids); pH 7.5)
50% v/v Precipitant Mix 1 (40% v/v PEG 500* MME; 20% w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 1.92 36.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.078 α = 90 b = 56.257 β = 90 c = 113.766 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 2024-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.7838 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.61 43.08 99.9 1 16.7 13.7 28739 24.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 0.903
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 1.75001 34.34 1.34 28653 1373 99.91 0.1855 0.1849 0.1858 0.1955 0.1962 34.42
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 5.7282 f_angle_d 0.8248 f_chiral_restr 0.0567 f_bond_d 0.0069 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2451 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing