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Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 2 M ammonium sulfate, 0.1 M BisTris-HCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K 2 VAPOR DIFFUSION, SITTING DROP 8 289 20% (w/v) polyethylene glycol 3350, and 0.2 M sodium citrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.954 α = 90 b = 108.648 β = 90 c = 166.384 γ = 90
Symmetry Space Group I 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 MARMOSAIC 225 mm CCD Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2012-11-16 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MARMOSAIC 300 mm CCD 2013-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM 2 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.89 30 99.9 0.077 22.8 6.4 17328 -3 67.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 2.99 99.5 0.783 2.1 6.1 1699
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD THROUGHOUT 2.893 29.547 1.34 17321 869 99.76 0.1944 0.1933 0.1964 0.2154 0.2161 Random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.072 f_angle_d 0.675 f_chiral_restr 0.041 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2141 Nucleic Acid Atoms 570 Solvent Atoms 100 Heterogen Atoms 67
Software Software Software Name Purpose HKL-2000 data collection SGXPRO model building PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling SGXPRO phasing