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GTP binding protein YsxC from Staphylococcus aureus
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 7.2 295.15 2.6M Potassium/sodium phosphate pH 7.6
Crystal Properties Matthews coefficient Solvent content 1.94 36.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.942 α = 90 b = 55.942 β = 90 c = 107.112 γ = 120
Symmetry Space Group P 32 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 80 PIXEL RIGAKU HyPix-6000HE 2022-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU PhotonJet-S 1.54184
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 20.05 99.6 0.087 0.098 0.044 0.998 11.3 7.7 13613
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 2 20.05 0.049 0.054 0.021 0.999 8.3
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 20.046 13539 708 99.245 0.26 0.257 0.2569 0.3165 0.3168 37.306
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] 2.787 2.787 -5.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.973 r_dihedral_angle_3_deg 14.535 r_dihedral_angle_1_deg 9.176 r_dihedral_angle_2_deg 7.999 r_lrange_it 7.775 r_lrange_other 7.773 r_mcangle_it 5.655 r_mcangle_other 5.652 r_scangle_it 4.934 r_scangle_other 4.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.973 r_dihedral_angle_3_deg 14.535 r_dihedral_angle_1_deg 9.176 r_dihedral_angle_2_deg 7.999 r_lrange_it 7.775 r_lrange_other 7.773 r_mcangle_it 5.655 r_mcangle_other 5.652 r_scangle_it 4.934 r_scangle_other 4.932 r_mcbond_it 3.953 r_mcbond_other 3.95 r_scbond_it 3.404 r_scbond_other 3.402 r_angle_refined_deg 2.058 r_angle_other_deg 1.008 r_nbd_refined 0.164 r_nbtor_refined 0.141 r_symmetry_nbd_other 0.127 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.119 r_symmetry_xyhbond_nbd_refined 0.093 r_symmetry_nbd_refined 0.087 r_nbd_other 0.083 r_symmetry_nbtor_other 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1488 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement REFMAC refinement CrysalisPro data collection Coot model building PHASER phasing CrysalisPro data reduction CrysalisPro data scaling