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Crystal structure of the Mycobacterium tuberculosis regulator VirS (N-terminal fragment 4-208) in complex with the lead compound SMARt751
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:SMART751 ratio 1:1, in situ proteolysis with subtilisin, temperature 293K, vapor diffusion
Crystal Properties Matthews coefficient Solvent content 2.33 47.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.332 α = 90 b = 115.332 β = 90 c = 70.987 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 1.692 19.295 96.5 0.17 0.179 0.056 0.997 9.6 10.1 51863
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 1.692 1.767 77.3 1.68 1.778 0.576 0.56 9.4
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 1.692 19.295 51863 2583 86.463 0.187 0.1855 0.1958 0.2168 0.2247 20.15
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] -0.035 -0.018 -0.035 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.402 r_dihedral_angle_3_deg 14.756 r_dihedral_angle_2_deg 7.35 r_lrange_it 6.398 r_lrange_other 6.385 r_dihedral_angle_1_deg 6.362 r_scangle_it 5.347 r_scangle_other 5.346 r_scbond_other 3.496 r_scbond_it 3.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.402 r_dihedral_angle_3_deg 14.756 r_dihedral_angle_2_deg 7.35 r_lrange_it 6.398 r_lrange_other 6.385 r_dihedral_angle_1_deg 6.362 r_scangle_it 5.347 r_scangle_other 5.346 r_scbond_other 3.496 r_scbond_it 3.494 r_mcangle_it 3.332 r_mcangle_other 3.332 r_mcbond_it 2.282 r_mcbond_other 2.28 r_angle_refined_deg 1.673 r_angle_other_deg 0.557 r_nbd_refined 0.221 r_nbd_other 0.201 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.12 r_xyhbond_nbd_refined 0.106 r_symmetry_nbd_refined 0.094 r_ncsr_local_group_1 0.088 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3172 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement autoPROC data processing Aimless data scaling STARANISO data scaling PHASER phasing autoPROC data reduction