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Naegleria gruberi RNA Ligase K170M mutant with AMP and Mn
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5COT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 NgRnlK170M (9.8 mg/ml) was adjusted to 5 mM AMP and 2 mM MnCl2 and incubated for 15 min on ice before aliquots of the protein solution (1 ul) were mixed on a coverslip with an equal volume of precipitant solution containing 0.1 M HEPES pH 6.5, 30% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.3 46.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.916 α = 90 b = 54.916 β = 90 c = 102.244 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 30 86.6 0.093 0.116 0.068 10.8 2.2 28362
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 46.9 0.247 0.341 0.234 0.779 1.3
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 THROUGHOUT 5COT 2.1 27.7 2.04 28362 2827 70.1 0.1955 0.189 0.1924 0.2531 0.2471 37.6561
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2691 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 24
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing