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Crystal structure of the Staphylococcus aureus GTPase Era in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 295.15 0.228M tri-Potassium citrate pH 8.3, 25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 5.44 77.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.146 α = 90 b = 78.146 β = 90 c = 244.905 γ = 90
Symmetry Space Group P 41 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 80 PIXEL DECTRIS PILATUS 2M 2024-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.977 LNLS SIRIUS MANACA
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 2.76 48.2 99.5 0.025 0.036 0.025 1 15.3 2 20362
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 2.76 2.86 94.7 1.037 0.417 0.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.76 48.195 20348 1018 99.569 0.173 0.1698 0.1698 0.2236 0.2234 98.104
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] -3.498 -3.498 6.996
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 35.594 r_lrange_other 35.582 r_scangle_it 29.524 r_scangle_other 29.516 r_mcangle_other 28.864 r_mcangle_it 28.861 r_scbond_it 20.083 r_scbond_other 20.065 r_mcbond_it 19.715 r_mcbond_other 19.707
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 35.594 r_lrange_other 35.582 r_scangle_it 29.524 r_scangle_other 29.516 r_mcangle_other 28.864 r_mcangle_it 28.861 r_scbond_it 20.083 r_scbond_other 20.065 r_mcbond_it 19.715 r_mcbond_other 19.707 r_dihedral_angle_3_deg 17.819 r_dihedral_angle_2_deg 14.724 r_dihedral_angle_6_deg 14.595 r_dihedral_angle_1_deg 10.179 r_rigid_bond_restr 4.918 r_angle_refined_deg 2.57 r_angle_other_deg 1.29 r_dihedral_angle_other_2_deg 0.538 r_nbd_refined 0.14 r_chiral_restr 0.136 r_nbtor_refined 0.131 r_symmetry_nbd_other 0.103 r_symmetry_xyhbond_nbd_refined 0.09 r_nbd_other 0.082 r_xyhbond_nbd_refined 0.072 r_symmetry_nbtor_other 0.06 r_symmetry_nbd_refined 0.053 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2404 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data scaling Coot model building