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Crystal Structure of MftR from mycobacterium tuberculosis
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 8.5 289 0.1 M Tris-HCl, and 2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.47 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.75 α = 90 b = 81.43 β = 107.356 c = 120.457 γ = 90
Symmetry Space Group I 1 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 100 CCD ADSC QUANTUM 315r 2022-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97902 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.7 47.38 95.7 0.996 10.9 3.8 27862
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 0.688 2.2 3.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT AlphaFold 2.7 47.38 27861 1380 99.376 0.231 0.2291 0.2295 0.2783 0.2788 48.104
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] -0.289 0.47 1.699 -1.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.408 r_dihedral_angle_2_deg 17.562 r_dihedral_angle_6_deg 15.213 r_lrange_it 11.291 r_scangle_it 7.814 r_mcangle_it 7.504 r_dihedral_angle_1_deg 6.333 r_scbond_it 5.319 r_mcbond_it 5.006 r_angle_refined_deg 1.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.408 r_dihedral_angle_2_deg 17.562 r_dihedral_angle_6_deg 15.213 r_lrange_it 11.291 r_scangle_it 7.814 r_mcangle_it 7.504 r_dihedral_angle_1_deg 6.333 r_scbond_it 5.319 r_mcbond_it 5.006 r_angle_refined_deg 1.899 r_symmetry_xyhbond_nbd_refined 0.921 r_symmetry_nbd_refined 0.357 r_nbtor_refined 0.293 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.11 r_gen_planes_refined 0.011 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7237 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASES phasing