☰ Navigation Tabs
Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase in complex with Tefuryltrione (Mn)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 Morpheus G12
0.1 M Carboxylic acids
0.1 M Buffer System 3 8.5
37.5 % v/v Precipitant Mix 4
Crystal Properties Matthews coefficient Solvent content 2.2 44.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.192 α = 90 b = 84.068 β = 100.51 c = 62.644 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 2024-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 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 1.7 35.32 98.7 0.089 0.096 0.036 0.998 10 7.1 42619 25.421
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 1.7 1.73 98.6 1.193 1.285 0.473 0.61 1.3 7.3
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 1.7 35.31 1.34 42566 2122 98.36 0.1747 0.1734 0.1758 0.1991 0.2004
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 21.376 f_angle_d 1.014 f_chiral_restr 0.097 f_plane_restr 0.01 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2948 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing