☰ Navigation Tabs
Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Topramezone (Mn)
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 VAPOR DIFFUSION 290 Morpheus H9,
0.1 M Amino acids,
0.1 M Buffer System 3 8.5,
30 % v/v Precipitant Mix 1
Crystal Properties Matthews coefficient Solvent content 3.08 60.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.2 α = 90 b = 149.95 β = 106.754 c = 87.763 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 2025-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.94056 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 67.63 100 0.058 0.069 0.036 0.999 13.6 7 117150 25.54
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 1.194 1.408 0.741 0.716 1.2
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 55.95 1.34 116989 5963 99.67 0.1665 0.1652 0.1679 0.19 0.1916 35.47
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 18.555 f_angle_d 1.3914 f_chiral_restr 0.1219 f_bond_d 0.0165 f_plane_restr 0.0118
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5340 Nucleic Acid Atoms Solvent Atoms 751 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing