☰ Navigation Tabs
Crystal structure of E. coli ApaH bound to Manganese ions
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, 2 mM MnCl2, 25 mM Hepes (pH 7.5), 0.2 M NaCl.
Well solution: 0.1 M Hepes (pH 7.5), 1.0 M Ammonium sulfate, 0.5% PEG8K.
Crystal Properties Matthews coefficient Solvent content 3.37 63.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.067 α = 90 b = 54.851 β = 130.12 c = 120.527 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 2019-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 1.362500 APS 24-ID-E
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 1.68 83.36 96.5 0.106 0.993 9 4.6 92329 16.6
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 1.68 1.71 87 0.602 0.665 1.7 4.4
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 1.68 83.36 1.35 92329 3846 94.33 0.1819 0.1816 0.1824 0.1931 0.1932 20.47
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 12.9657 f_angle_d 0.9583 f_chiral_restr 0.0585 f_plane_restr 0.0249 f_bond_d 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4210 Nucleic Acid Atoms Solvent Atoms 690 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement Coot model building Aimless data scaling XDS data reduction PHASER phasing