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12-oxophytodienoate reductase 3 (OPR3) from Solanum lycopersicum in complex with 2-methoxyethyl (Z)-2-(hydroxyimino)-3-oxobutanoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 100 mM amino acid mix (0.02M DL-Glutamic acid monohydrate; 0.02M DL-Alanine; 0.02M Glycine; 0.02M DL-Lysine monohydrochloride; 0.02M DL-Serine), 20% v/v Ethylene glycol; 10 % w/v PEG 8000, 100 mM Tris (base), BICINE pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.21 44.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.719 α = 90 b = 89.026 β = 100.274 c = 90.074 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 2M 2021-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
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 1.82 46.48 90.44 0.993 6.25 1.6 123419 21.23
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 1.82 1.885 0.677
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3hgs 1.82 46.48 1.04 68067 1157 97.69 0.1722 0.1717 0.2048 0.2052 24.21
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 14.5146 f_angle_d 0.8186 f_chiral_restr 0.0531 f_bond_d 0.0063 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5734 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 121
Software Software Software Name Purpose PHENIX refinement AutoProcess data processing XDS data reduction Aimless data scaling PHASER phasing