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Crystal structure of the double mutant (D52N/L375F) of the full-length NT5C2 in the active state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DDK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 2M ammonium sulfate and 5% (v/v) 2-proponal, 5 mM ATP, 5 mM IMP, and 5 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 3 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.53 α = 90 b = 126.717 β = 90 c = 130.198 γ = 90
Symmetry Space Group I 2 2 2
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 2015-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.977 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 48.935 100 0.08 0.09 0.03 0.98 35.2 14.7 44471 30.64
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 2.15 100 0.53 0.55 0.14 0.95 4.9 14.8
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 6DDK 2.1 48.935 1.34 44471 4448 99.96 0.1563 0.1532 0.156 0.1836 0.1856
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 14.07 f_angle_d 0.836 f_chiral_restr 0.052 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3848 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling COMO phasing