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Low molecular weight antigen MTB12
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 293.15 1.8 M Ammonium sulfate, 0.1 M Citric acid pH 3.7
Crystal Properties Matthews coefficient Solvent content 4.5 72.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.67 α = 90 b = 100.67 β = 90 c = 98.53 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 125 PIXEL STFC Large Pixel Detector 2023-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97942 PAL/PLS 5C (4A)
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 2.68 29.84 99.82 0.999 22.6 26.1 14762
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 2.68 2.776 0.768
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 FREE R-VALUE AlphaFold 2.68 29.84 14755 739 99.831 0.279 0.2777 0.2721 0.304 0.3054 94.44
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] -3.579 -3.579 7.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.219 r_dihedral_angle_4_deg 18.721 r_dihedral_angle_3_deg 17.628 r_lrange_it 12.672 r_lrange_other 12.669 r_scangle_it 10.716 r_scangle_other 10.704 r_mcangle_it 9.832 r_mcangle_other 9.828 r_scbond_it 7.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.219 r_dihedral_angle_4_deg 18.721 r_dihedral_angle_3_deg 17.628 r_lrange_it 12.672 r_lrange_other 12.669 r_scangle_it 10.716 r_scangle_other 10.704 r_mcangle_it 9.832 r_mcangle_other 9.828 r_scbond_it 7.276 r_scbond_other 7.273 r_mcbond_other 6.463 r_mcbond_it 6.462 r_dihedral_angle_1_deg 6.045 r_angle_other_deg 2.395 r_angle_refined_deg 1.813 r_nbd_other 0.33 r_symmetry_nbd_other 0.254 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.181 r_symmetry_nbd_refined 0.154 r_symmetry_xyhbond_nbd_other 0.104 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.081 r_bond_other_d 0.037 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1620 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing