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Human AdoMetDC with covalently bound 5'-[(2-aminooxyethyl)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 1.92 35.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.778 α = 90 b = 44.458 β = 104.17 c = 70.554 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 IMAGE PLATE RIGAKU RAXIS IV++ 2005-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.43 30 93.6 0.09 0.09 10.9 2.5 10403 10051 31.4
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) 2.43 2.52 86.8 0.338 0.338 2.9 1.9 950
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 2.43 18.78 10403 10051 527 90.3 0.199 0.199 0.199 0.2018 0.247 0.2447 RANDOM 31.596
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] -4.11 6.07 9.48 -5.37
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.2 c_scangle_it 2.66 c_mcangle_it 2.3 c_scbond_it 1.83 c_angle_deg 1.4 c_mcbond_it 1.34 c_improper_angle_d 1.28 c_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2423 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 31
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