☰ Navigation Tabs
The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI in a Complex with Substrate-like DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other low resolution SAD determined structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 289 PEG 3350
ammonium tartrate
BisTris buffer
calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.673 α = 90 b = 147.133 β = 94.34 c = 103.485 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 300 mm CCD 2013-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97919 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 3.29 35.09 99.9 0.211 6.4 4.7 24388 82.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.29 3.41 99.8 2 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE low resolution SAD determined structure 3.301 35.09 1.35 47324 2340 97.88 0.2426 0.24 0.2423 0.2934 0.2964
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 15.797 f_angle_d 0.664 f_chiral_restr 0.027 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10386 Nucleic Acid Atoms 1269 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement