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Crystal structure of dicamba monooxygenase bound to dicamba
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GKE PDB entry 3GKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 5% PEG 4000, 100 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.62 53.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.323 α = 90 b = 81.323 β = 90 c = 159.282 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 ADSC QUANTUM 315 Bent Rh coated conical Si mirror 2007-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 36 98.41 0.073 23.1 7.4 68055 67158
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 100 0.64 2.5 4.9 6814
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3GKE 2.1 36 68055 67158 3338 98.41 0.19262 0.18974 0.1942 0.24701 0.2496 RANDOM 40.721
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] 0.1 0.05 0.1 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_dihedral_angle_4_deg 18.719 r_dihedral_angle_3_deg 17.114 r_dihedral_angle_1_deg 8.969 r_scangle_it 5.22 r_scbond_it 4.047 r_mcangle_it 2.429 r_mcbond_it 2.052 r_angle_refined_deg 1.134 r_angle_other_deg 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.358 r_dihedral_angle_4_deg 18.719 r_dihedral_angle_3_deg 17.114 r_dihedral_angle_1_deg 8.969 r_scangle_it 5.22 r_scbond_it 4.047 r_mcangle_it 2.429 r_mcbond_it 2.052 r_angle_refined_deg 1.134 r_angle_other_deg 0.68 r_mcbond_other 0.651 r_symmetry_vdw_other 0.285 r_nbd_other 0.244 r_nbd_refined 0.235 r_metal_ion_refined 0.214 r_symmetry_hbond_refined 0.197 r_nbtor_refined 0.19 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.181 r_nbtor_other 0.09 r_chiral_restr 0.08 r_xyhbond_nbd_other 0.059 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7663 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 40
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling