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Crystal structure of E. coli ApaH in complex with Ap4AG
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, 4 mM MgCl2, 10 mM Ca(OAc)2, 25 mM Hepes (pH 7.5), 0.2 M NaCl and soaked with Ap4AG. Well solution: 0.2 M Trisodium Citrate, 20% PEG3350.
Crystal Properties Matthews coefficient Solvent content 3.49 64.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.581 α = 90 b = 55.04 β = 130.23 c = 120.581 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 EIGER2 X 16M 2021-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97911 APS 24-ID-C
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 1.88 63.59 97.5 0.187 0.99 4.5 5.1 65917 31.84
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 1.88 1.93 89.7 1.746 0.308 0.6 4.7
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 1.89 50.51 1.33 65917 3835 94.65 0.2422 0.2409 0.2438 0.2844 0.285
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 11.96 f_angle_d 1.16 f_chiral_restr 0.064 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4193 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 99
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction Coot model building PHASER phasing