☰ Navigation Tabs
Crystal structure of Carminomycin-4-O-methyltransferase (DnrK) in complex with S-adenosyl-L-homocystein (SAH) and 4-methoxy-e-rhodomycin T (M-ET)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other RdmB+SAM+DbrA complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 ammonium sulphate, MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.69 α = 90 b = 53.134 β = 105.03 c = 83.07 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 MARRESEARCH 2003-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.09 MAX II I711
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 2.35 35 94.8 0.071 13.9 7 41714 41714 29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.35 2.411 89.8 0.214 5.5
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 RdmB+SAM+DbrA complex 2.35 35 33956 1829 95.61 0.19593 0.1933 0.2049 0.24384 0.2514 RANDOM 27.453
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] -2.24 0.32 1.59 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.963 r_scangle_it 2.511 r_scbond_it 1.453 r_angle_refined_deg 1.423 r_angle_other_deg 1.024 r_mcangle_it 0.914 r_mcbond_it 0.465 r_symmetry_hbond_refined 0.239 r_nbd_other 0.233 r_symmetry_vdw_other 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.963 r_scangle_it 2.511 r_scbond_it 1.453 r_angle_refined_deg 1.423 r_angle_other_deg 1.024 r_mcangle_it 0.914 r_mcbond_it 0.465 r_symmetry_hbond_refined 0.239 r_nbd_other 0.233 r_symmetry_vdw_other 0.222 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.105 r_nbtor_other 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 5254 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing