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Crystal structure of DndE G21/24K mutant involved in DNA phosphorothioation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291.15 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 0.2 M Potassium sodium tartrate tetrahydrate, 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.11 41.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.297 α = 90 b = 57.297 β = 90 c = 130.222 γ = 90
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 315r 2014-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U
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 2.9 50 97.6 0.135 6.3 3.5 9087
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 2.9 3 99.2 0.516 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.9 50.01 8623 432 97.61 0.2273 0.2252 0.2091 0.272 0.2384 RANDOM 42.31
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] 0.61 0.61 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.874 r_sphericity_bonded 26.971 r_dihedral_angle_3_deg 17.985 r_dihedral_angle_4_deg 14.918 r_dihedral_angle_1_deg 4.828 r_rigid_bond_restr 2.406 r_angle_refined_deg 1.196 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3114 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data scaling HKL-2000 data reduction PHENIX phasing HKL data scaling