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Structure of S. aureus Rel catalytic domains in complex with pppGpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.16 6% w/vPEG 3350
0.15 M Sodium chloride
0.4 M Potassium iodide
pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.48 64.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.41 α = 90 b = 132.54 β = 103.59 c = 73.47 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 12M 2019-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.63 42.25 99.4 0.18 0.07 0.993 8.2 7.3 31024 59.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.63 2.72 1.21 0.47 0.667 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6S2U 2.63 42.25 1.38 31024 1550 99.19 0.2171 0.2149 0.2228 0.2608 0.2657
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 23.049 f_angle_d 0.741 f_chiral_restr 0.047 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5204 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 218
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing