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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 8.5 294 PEG4000, sodium acetate, Tris-buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.6 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.682 α = 90 b = 102.582 β = 90 c = 124.256 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 MARRESEARCH 2003-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.98 ESRF ID29
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 2.5 79.06 99.9 0.104 12.4 8.9 27569 27569 31
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) 2.5 2.565 99.9 0.322 4.5
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 RdmB+SAM+DbrA complex 2.5 54 26156 26156 1387 99.93 0.2064 0.2064 0.20296 0.2136 0.27052 0.272 RANDOM 25.953
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] -1.59 -1.13 2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.744 r_scangle_it 2.25 r_angle_refined_deg 1.531 r_scbond_it 1.311 r_angle_other_deg 1.001 r_mcangle_it 0.939 r_mcbond_it 0.495 r_symmetry_vdw_other 0.3 r_nbd_other 0.231 r_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.744 r_scangle_it 2.25 r_angle_refined_deg 1.531 r_scbond_it 1.311 r_angle_other_deg 1.001 r_mcangle_it 0.939 r_mcbond_it 0.495 r_symmetry_vdw_other 0.3 r_nbd_other 0.231 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.215 r_xyhbond_nbd_refined 0.199 r_symmetry_hbond_refined 0.103 r_chiral_restr 0.092 r_nbtor_other 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5309 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing