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Crystal structure of itaconate modified Mycobaterium tuberculosis isocitrate lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 20% PEG3350, 0.2M sodium nitrate, 0.1M bis-tris propane
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.314 α = 90 b = 133.171 β = 90 c = 159.318 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2019-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953733 Australian Synchrotron MX2
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 1.55 49.377 99.7 0.123 0.128 0.034 0.999 11.6 13.8 242871
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 1.55 1.58 99 2.057 2.133 0.56 0.613 1.4 14.1
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 1F8I 1.55 49.377 242747 12123 99.574 0.159 0.1584 0.1701 0.1791 0.1876 21.236
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] -0.679 -0.093 0.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.359 r_dihedral_angle_4_deg 17.312 r_dihedral_angle_3_deg 11.779 r_dihedral_angle_1_deg 6.285 r_lrange_it 5.375 r_lrange_other 5.277 r_scangle_it 4.597 r_scangle_other 4.596 r_scbond_other 3.099 r_scbond_it 3.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.359 r_dihedral_angle_4_deg 17.312 r_dihedral_angle_3_deg 11.779 r_dihedral_angle_1_deg 6.285 r_lrange_it 5.375 r_lrange_other 5.277 r_scangle_it 4.597 r_scangle_other 4.596 r_scbond_other 3.099 r_scbond_it 3.098 r_mcangle_it 2.399 r_mcangle_other 2.399 r_mcbond_it 1.833 r_mcbond_other 1.826 r_angle_other_deg 1.427 r_angle_refined_deg 1.303 r_nbd_refined 0.208 r_nbd_other 0.207 r_symmetry_nbd_refined 0.181 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.127 r_symmetry_xyhbond_nbd_refined 0.11 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.069 r_ncsr_local_group_4 0.058 r_ncsr_local_group_2 0.056 r_ncsr_local_group_5 0.05 r_ncsr_local_group_3 0.048 r_ncsr_local_group_1 0.047 r_ncsr_local_group_6 0.047 r_chiral_restr_other 0.016 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13198 Nucleic Acid Atoms Solvent Atoms 1770 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing