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Crystal structure of E. coli diadenosine tetraphosphate hydrolase (ApaH)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 Conditions: 0.3 mM ApaH (10 mg/mL), 1 mM DTT, 10 mM MgCl2, 25 mM Hepes (pH 7.5), 0.2 M NaCl.
Well solution: 0.1 M Bis-tris (pH 6.5), 0.3 M Sodium potassium tartrate, 18% PEG3350.
Crystal Properties Matthews coefficient Solvent content 3.43 64.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.764 α = 90 b = 55.224 β = 129.57 c = 120.388 γ = 90
Symmetry Space Group C 1 2 1
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 2020-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97930 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.77 28.56 99.5 0.074 0.996 12 5.7 82849 27.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.81 94.4 0.67 0.757 1.9 5.5
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 1.77 28.56 1.34 82838 2000 99.45 0.183 0.1826 0.1827 0.1983 0.1977 30.91
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 15.1971 f_angle_d 0.9477 f_chiral_restr 0.0578 f_plane_restr 0.0106 f_bond_d 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4198 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement XDS data reduction FAST_DP data scaling Coot model building PHASER phasing