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Crystal structure of the tylM1 N,N-dimethyltransferase in complex with SAH and TDP-Qui3NMe2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PFH PDB ENTRY 3PFH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 9 293 15-20% PEG3400, 200 mM sodium chloride, 5 mM S-adenosylhomocysteine, 10 mM TDP-3-N,N-dimethylamino-3,6-dideoxyglucose, pH 9, batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.532 α = 90 b = 92.05 β = 106.1 c = 80.177 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 CCD ADSC QUANTUM 210r 2012-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.98789 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 91.6 0.069 0.069 43.2 4.3 123048 123048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 79.6 0.176 0.176 4.3 2.4 5330
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 PHASER THROUGHOUT PDB ENTRY 3PFH 1.6 41.24 123048 123048 6150 91.42 0.18231 0.18056 0.1902 0.21602 0.2278 RANDOM 24.063
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] 0.14 -2.21 -0.02 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.448 r_dihedral_angle_4_deg 20.249 r_dihedral_angle_3_deg 13.57 r_dihedral_angle_1_deg 6.823 r_angle_refined_deg 2.025 r_angle_other_deg 0.874 r_chiral_restr 0.114 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.448 r_dihedral_angle_4_deg 20.249 r_dihedral_angle_3_deg 13.57 r_dihedral_angle_1_deg 6.823 r_angle_refined_deg 2.025 r_angle_other_deg 0.874 r_chiral_restr 0.114 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.001 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7317 Nucleic Acid Atoms Solvent Atoms 647 Heterogen Atoms 252
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling