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Human AdoMetDC with 5'-[(2-carboxamidoethyl)methylamino]-5'-deoxy-8-methyladenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I7B 1I7B.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 16% PEG 8000, 100 mM Tris, 10 mM DTT, pH 8.0, vapor diffusion, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.2 44.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.818 α = 90 b = 50.949 β = 105.52 c = 68.985 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 ADSC QUANTUM 210 2006-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9790 CHESS A1
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 1.84 50 97.6 0.06 0.06 17.4 3.2 28243 27656 16.9
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) 1.84 1.91 94.1 0.14 0.14 8 2.6 2724
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 THROUGHOUT 1I7B.pdb 1.84 45.11 28243 27656 1337 95.1 0.204 0.204 0.204 0.2042 0.237 0.2353 RANDOM 26.542
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] 10.65 -3.2 -2.42 -8.23
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.3 c_scangle_it 3.01 c_mcangle_it 2.18 c_scbond_it 2.05 c_mcbond_it 1.35 c_angle_deg 1.3 c_improper_angle_d 1.08 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2494 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 32
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction CNS phasing