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Crystal structure of the Escherichia coli nucleosidase PpnN (E264A, pppGpp form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 6 mg/ml
0.4 KNa tartrate
Crystal Properties Matthews coefficient Solvent content 3.39 63.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.919 α = 90 b = 156.919 β = 90 c = 224.654 γ = 90
Symmetry Space Group P 43 21 2
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 S 16M 2019-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97623 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 3.4 47.42 99.83 0.18 0.98 6.92 2 39210 101.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.62 99.6 1.11 0.52 1.01
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 3.4 47.42 1.34 39210 396 99.85 0.2211 0.2205 0.2154 0.2779 0.2779 103.78
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 9.9868 f_angle_d 1.425 f_chiral_restr 0.0755 f_bond_d 0.0143 f_plane_restr 0.0117
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14181 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing