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x-ray structure of the KijD1 C3-methyltransferase from Actinomadura kijaniata in complex with SAH and dTDP-sugar product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 20-23% PEG-3350, 100 mM MOPS, 100 mM MgCl2, 10 mM dTDP, 5 mM SAH
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.088 α = 90 b = 108.893 β = 90 c = 142.783 γ = 90
Symmetry Space Group P 21 21 21
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 Bruker Platinum 135 2015-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 1.6 50 96.4 0.079 9 3.6 102095
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) 1 1.6 1.7 88.5 0.352 2.1 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 5t64 1.6 30 97001 5084 96.47 0.20081 0.19834 0.2072 0.24906 0.2572 RANDOM 22.306
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] -1.17 0.65 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.814 r_dihedral_angle_4_deg 17.759 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_1_deg 6.934 r_long_range_B_refined 6.382 r_long_range_B_other 6.382 r_scangle_other 4.655 r_mcangle_it 3.54 r_mcangle_other 3.54 r_scbond_it 3.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.814 r_dihedral_angle_4_deg 17.759 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_1_deg 6.934 r_long_range_B_refined 6.382 r_long_range_B_other 6.382 r_scangle_other 4.655 r_mcangle_it 3.54 r_mcangle_other 3.54 r_scbond_it 3.302 r_scbond_other 3.302 r_mcbond_it 2.663 r_mcbond_other 2.663 r_angle_refined_deg 2.137 r_angle_other_deg 1.056 r_chiral_restr 0.135 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6278 Nucleic Acid Atoms Solvent Atoms 784 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing