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Crystal structure of apo Dicamba Monooxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GTE PDB entry 3GTE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 10-20 mg/mL protein in 25 mM Tris-HCl, pH 8.0, 10 mM sodium chloride, 0.1 mM EDTA, trace PMSF + 1:1 reservoir solution (15-20% w/v PEG6000, 100 mM sodium citrate, pH 6.0) in 2-6 uL droplet
Crystal Properties Matthews coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.17 α = 90 b = 80.17 β = 90 c = 159.346 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU CuVarimax HR 2005-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 3 50 99.6 0.075 25.8 8.1 45738 52.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 100 0.304 6.69 7.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3GTE 3 19.26 1.97 45620 4055 99.87 0.1979 0.1926 0.1987 0.2517 0.2515 53.2
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 7.8553 f_angle_d 1.2777 f_chiral_restr 0.0687 f_bond_d 0.0098 f_plane_restr 0.0087
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7525 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 12
Software Software Software Name Purpose CNX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing