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Crystal structure of E. coli ApaH in complex with Ap4G
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 in Ap4G.
Well solution: 0.1 M Hepes (pH 7.5), 1.0 M Ammonium sulfate, 0.5% PEG8K.
Crystal Properties Matthews coefficient Solvent content 3.54 65.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.636 α = 90 b = 55.128 β = 130.04 c = 120.798 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 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97932 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 1.55 28.51 98.5 0.063 0.998 12.2 4.8 121613 19.44
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 1.55 1.59 89.9 0.604 0.741 1.8 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 1.55 28.51 1.35 121609 1996 98.33 0.1668 0.1664 0.1665 0.1905 0.1905
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 5.832 f_angle_d 0.975 f_chiral_restr 0.064 f_plane_restr 0.009 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4226 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms 116
Software Software Software Name Purpose PHENIX refinement FAST_DP data scaling XDS data reduction Coot model building PHASER phasing