☰ Navigation Tabs
Crystal structure of the Mycobacterium tuberculosis regulator VirS (N-terminal fragment 4-208) in complex with the drug candidate alpibectir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P9WMJ3-F1 residues 1-230
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.3 M sodium acetate trihydrate, 0.1 M Tris, pH 7.5, 8% (w/v) PEG 20,000, 8% (v/v) PEG 500 MME, pH7.5, protein:alpibectir ratio 1:1, in situ proteolysis with subtilisin, temperature 293K, vapor diffusion
Crystal Properties Matthews coefficient Solvent content 2.68 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.313 α = 90 b = 115.313 β = 90 c = 70.713 γ = 120
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 PILATUS3 6M 2023-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
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 1.494 19.244 96.3 0.157 0.172 0.068 0.977 6.5 6.2 78828
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 1.494 1.535 92.4 0.88 0.965 0.387 0.106 2 6.4
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 THROUGHOUT 1.494 19.244 78828 3979 91.009 0.181 0.1798 0.181 0.2043 0.1819 18.895
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] -0.005 -0.003 -0.005 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.699 r_dihedral_angle_3_deg 14.102 r_dihedral_angle_2_deg 11.056 r_dihedral_angle_1_deg 6.849 r_lrange_it 6.751 r_lrange_other 6.744 r_scangle_it 6.079 r_scangle_other 6.078 r_scbond_it 4.222 r_scbond_other 4.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.699 r_dihedral_angle_3_deg 14.102 r_dihedral_angle_2_deg 11.056 r_dihedral_angle_1_deg 6.849 r_lrange_it 6.751 r_lrange_other 6.744 r_scangle_it 6.079 r_scangle_other 6.078 r_scbond_it 4.222 r_scbond_other 4.221 r_mcangle_it 3.161 r_mcangle_other 3.16 r_mcbond_it 2.267 r_mcbond_other 2.264 r_angle_refined_deg 2.129 r_angle_other_deg 0.681 r_nbd_other 0.302 r_symmetry_nbd_refined 0.246 r_nbd_refined 0.238 r_symmetry_xyhbond_nbd_refined 0.212 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.187 r_xyhbond_nbd_other 0.134 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.107 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3166 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling Aimless data scaling PHASER phasing