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MenT1 toxin (rv0078a) from Mycobacterium tuberculosis H37Rv, phosphorylated at T39
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 4 M Sodium Formate, 0.1 M Tris, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.59 65.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.001 α = 90 b = 127.001 β = 90 c = 68.776 γ = 90
Symmetry Space Group I 4 2 2
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 EIGER2 XE 16M 2023-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.8 63.58 100 0.014 0.02 1 27.4 1.8 7213 71.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 100 0.074 0.105 0.992 3.5 1.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.8 63.58 6853 361 99.99 0.19906 0.19683 0.2091 0.23939 0.247 RANDOM 77.14
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] -6.75 -6.75 13.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.531 r_long_range_B_refined 14.309 r_long_range_B_other 14.304 r_scangle_other 11.223 r_mcangle_other 8.523 r_mcangle_it 8.492 r_dihedral_angle_1_deg 7.473 r_scbond_it 7.336 r_scbond_other 7.333 r_dihedral_angle_2_deg 6.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.531 r_long_range_B_refined 14.309 r_long_range_B_other 14.304 r_scangle_other 11.223 r_mcangle_other 8.523 r_mcangle_it 8.492 r_dihedral_angle_1_deg 7.473 r_scbond_it 7.336 r_scbond_other 7.333 r_dihedral_angle_2_deg 6.664 r_mcbond_it 5.713 r_mcbond_other 5.649 r_angle_refined_deg 1.48 r_angle_other_deg 0.481 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1357 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing