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DNA ligase from the archaeon Thermococcus sp. 1519
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GDE pdb entry 3GDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 7.5 291 0.1 Na Cacodilate, 0.2 M MgCl2, 20% Glicerol, 16% PEG 8000, 100 mM NaCl, 50mM Tris-HCl, Protein 22mg/mL (protein buffer: 50mM Tris-Hcl, 100 mM NaCl, 0.5 DTT), Gel-tube counter-diffusion method, pH 7.5, LIQUID DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.69 54.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.95 α = 90 b = 85.6 β = 90 c = 105.96 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 MARMOSAIC 225 mm CCD The rhodium-coated mirrors 2010-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 29.257 97.8 25.09 4 14557 14237 -3
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 3.02 3.2 98.7 3.43
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 pdb entry 3GDE 3.018 29.257 1.35 14237 14229 715 99.69 0.2365 0.2326 0.2318 0.3096 0.3093
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] -7.2354 -5.8688 13.1043
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.768 f_angle_d 1.319 f_chiral_restr 0.086 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4123 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data collection BALBES phasing PHENIX refinement XDS data reduction XSCALE data scaling