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Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase in complex with Fenquinotrione (Mn)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Morpheus F4
0.12 M Monosaccharides
0.1 M Buffer System 1 6.5
37.5 % v/v Precipitant Mix 4
Crystal Properties Matthews coefficient Solvent content 2.12 41.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.103 α = 90 b = 83.445 β = 102.79 c = 61.25 γ = 90
Symmetry Space Group C 1 2 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 DECTRIS EIGER X 16M 2025-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 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 1.55 35.56 99.3 0.079 0.086 0.032 0.999 11.1 7 54361 20.562
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 1.55 1.58 99.4 1.122 1.216 0.463 0.739 6.8
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 1.55 35.56 1.34 54344 2637 99.12 0.1621 0.1611 0.1622 0.1814 0.1821
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 17.752 f_angle_d 1.415 f_chiral_restr 0.148 f_bond_d 0.016 f_plane_restr 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2957 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing