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Crystal Structure of Staphylococcus aureus RsgA bound to ppGpp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T9H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290.15 0.2 M Sodium Citrate, 0.1 M Bis-Tris Propane pH 6.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.67 53.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.45 α = 90 b = 66.929 β = 90 c = 114.158 γ = 90
Symmetry Space Group P 21 21 21
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 XE 16M 2018-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.94 57.74 99.9 0.158 0.165 0.046 0.998 11 12.8 29355
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.99 99.5 0.95 0.99 0.276 0.802 12.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1T9H 1.94 57.73 27838 1464 99.68 0.2163 0.2139 0.2251 0.2622 0.2664 RANDOM 32.011
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] -0.69 -1 1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.118 r_dihedral_angle_4_deg 17.207 r_dihedral_angle_3_deg 16.93 r_dihedral_angle_1_deg 7.316 r_angle_refined_deg 1.917 r_angle_other_deg 1.08 r_chiral_restr 0.111 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.118 r_dihedral_angle_4_deg 17.207 r_dihedral_angle_3_deg 16.93 r_dihedral_angle_1_deg 7.316 r_angle_refined_deg 1.917 r_angle_other_deg 1.08 r_chiral_restr 0.111 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2185 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHASER phasing