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X-ray structure of the C3-methyltransferase KijD1 from Actinomadura kijaniata in complex with TDP and SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NDI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 20-23% PEG-3350, 100 mM MgCl2, 100 mM MOPS, 10 mM dTDP, 5 mM SAH
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.34 α = 90 b = 110.894 β = 90 c = 143.251 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 2015-10-10 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 1.7 87.69 98 0.075 10.7 4.2 89296
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 1.7 1.8 92.4 0.338 2.5 2.4
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 MOLECULAR REPLACEMENT THROUGHOUT 3NDI 1.7 30 84825 4471 98.3 0.18273 0.18072 0.1912 0.22042 0.2264 RANDOM 21.704
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] -0.19 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.077 r_dihedral_angle_4_deg 19.64 r_dihedral_angle_3_deg 13.368 r_dihedral_angle_1_deg 6.399 r_long_range_B_other 6.15 r_long_range_B_refined 6.146 r_scangle_other 4.583 r_mcangle_it 3.149 r_mcangle_other 3.149 r_scbond_it 3.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.077 r_dihedral_angle_4_deg 19.64 r_dihedral_angle_3_deg 13.368 r_dihedral_angle_1_deg 6.399 r_long_range_B_other 6.15 r_long_range_B_refined 6.146 r_scangle_other 4.583 r_mcangle_it 3.149 r_mcangle_other 3.149 r_scbond_it 3.074 r_scbond_other 3.062 r_mcbond_it 2.258 r_mcbond_other 2.257 r_angle_refined_deg 1.712 r_angle_other_deg 0.892 r_chiral_restr 0.112 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 6227 Nucleic Acid Atoms Solvent Atoms 687 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing