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Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its product pppGpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DEC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Citric acid, pH 4.0,
5% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.05 59.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.869 α = 90 b = 113.492 β = 127.17 c = 139.848 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 PSI PILATUS 6M 2014-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97934 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.94 50.6 96.1 0.103 5.8 6.4 51454
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5DEC 2.942 50.567 51454 2634 98.11 0.1838 0.1805 0.1826 0.2449 0.2445
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 22.168 f_angle_d 1.441 f_chiral_restr 0.075 f_bond_d 0.014 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12532 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 484
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing