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Crystal structure of E. coli ApaH in complex with Ap4A
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, 5 mM MgCl2, 25 mM Hepes (pH 7.5), 0.2 M NaCl and soaked with Ap4A
Well solution: 0.2 M Sodium malonate, 20% PEG3350.
Crystal Properties Matthews coefficient Solvent content 3.44 64.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.716 α = 90 b = 55.321 β = 129.88 c = 120.974 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 2019-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 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 1.71 83.67 98.3 0.08 0.995 10.4 5 91253 31.6
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 1.71 1.73 89.1 1.739 0.253 0.6 4.9
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 1.71 83.67 1.34 91253 3835 95.6 0.1951 0.1946 0.1976 0.2186 0.2193 35.89
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 22.1676 f_angle_d 1.1193 f_chiral_restr 0.0576 f_bond_d 0.0082 f_plane_restr 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4220 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 91
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHASER phasing