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Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Gp5A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 Purified hAK3 was dialyzed against 30 mM MOPS buffer with 50 mM NaCl pH 7.0 and concentrated to 15-20 mg per ml. The resevoir contained 20% isopropanol, 0.1 M NaCitrate pH 5.6 and 20% PEG 4000. Drop size 1 plus 1 microliter.
Crystal Properties Matthews coefficient Solvent content 2.08 40.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.468 α = 93.79 b = 66.76 β = 93.95 c = 105.909 γ = 89.71
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 PILATUS3 6M 2018-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.822 45.36 93.1 0.064 0.093 0.995 7.3 1.9 103037
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.822 1.95 80.9 0.644 0.6 0.632 1.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1zd8 1.822 45.36 1.96 102997 5307 92.99 0.195 0.1916 0.2565 0.269 37.9739
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 10403 Nucleic Acid Atoms Solvent Atoms 798 Heterogen Atoms 354
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing