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Crystal structure of the N4BP2 polynucleotide kinase (PNK) domain in complex with ADP and Mg.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 Crystals were grown in 20% PEG 3350, 0.2 M ammonium sulfate, 0.1 M MES/imidazole (pH 6.0), 100 mM Mg2+, 2 mM ATP, 10% isopropanol, and 5% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.48 50.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.871 α = 90 b = 107.283 β = 90 c = 113.745 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 PIXEL DECTRIS EIGER X 16M 2024-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979338 NSLS-II 17-ID-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 1.95 33.813 100 0.088 0.093 0.032 0.999 14.1 8.6 46364
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 1.95 1.99 100 1.622 1.722 0.576 0.33 1.4 8.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.95 33.81 1.35 46356 2334 99.98 0.1752 0.1729 0.1739 0.2206 0.2205 52.39
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 19.1588 f_angle_d 1.3001 f_chiral_restr 0.0755 f_bond_d 0.0158 f_plane_restr 0.0104
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3891 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 149
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction