☰ Navigation Tabs
X-Ray crystal structure the N,N-dimethyltransferase TylM1 from Streptomyces fradiae in complex with SAM and dTDP-phenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BXO PDB ENTRY 3BXO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 22% monomethylether poly(ethylene glycol) 5000, 2% isopropanol, 100mM MOPS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.079 α = 90 b = 41.382 β = 121.21 c = 86.637 γ = 90
Symmetry Space Group C 1 2 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 Bruker Platinum 135 Montell 2010-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 1.349 100 94.3 0.047 0.047 13.7 3.2 55697 55697
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) 1.349 1.44 87.5 0.213 0.213 2.6 1.6 9141
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 (All) 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 3BXO 1.349 100 55697 52903 2794 94.37 0.18469 0.18469 0.18341 0.1776 0.20853 0.2016 RANDOM 16.587
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] -0.46 -0.19 0.51 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.131 r_dihedral_angle_4_deg 22.823 r_dihedral_angle_3_deg 14.8 r_dihedral_angle_1_deg 6.474 r_scangle_it 5.464 r_scbond_it 3.734 r_mcangle_it 2.612 r_angle_refined_deg 2.154 r_mcbond_it 1.692 r_chiral_restr 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.131 r_dihedral_angle_4_deg 22.823 r_dihedral_angle_3_deg 14.8 r_dihedral_angle_1_deg 6.474 r_scangle_it 5.464 r_scbond_it 3.734 r_mcangle_it 2.612 r_angle_refined_deg 2.154 r_mcbond_it 1.692 r_chiral_restr 0.149 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1836 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 62
Software Software Software Name Purpose PROTEUM PLUS data collection PHASER phasing REFMAC refinement SAINT data reduction SADABS data scaling