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Sulfatase from Mycobacterium tuberculosis (Rv3406) in complex with inhibitor FG2216
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FFA PDB entry 4FFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 16% PEG2000, 100 mM Tris, pH 8.5, 2% MPD, 300 mM magnesium nitrate
Crystal Properties Matthews coefficient Solvent content 2.21 44.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.04 α = 90 b = 129.006 β = 90 c = 138.355 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 291 PIXEL DECTRIS EIGER X 16M 2021-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.4 47.43 100 0.07 0.998 9.5 52.6 46395
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 2.4 2.48 100 0.652 1.6 52.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4FFA 2.4 47.43 46327 2281 99.937 0.249 0.2465 0.2624 0.2889 0.3034 taken from previous in-house structure 65.466
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] 9.709 -4.639 -5.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.963 r_dihedral_angle_6_deg 10.823 r_dihedral_angle_2_deg 6.737 r_dihedral_angle_1_deg 6.242 r_lrange_it 5.922 r_lrange_other 5.922 r_mcangle_it 3.833 r_mcangle_other 3.832 r_scangle_it 3.481 r_scangle_other 3.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.963 r_dihedral_angle_6_deg 10.823 r_dihedral_angle_2_deg 6.737 r_dihedral_angle_1_deg 6.242 r_lrange_it 5.922 r_lrange_other 5.922 r_mcangle_it 3.833 r_mcangle_other 3.832 r_scangle_it 3.481 r_scangle_other 3.48 r_mcbond_it 2.226 r_mcbond_other 2.224 r_scbond_it 2.118 r_scbond_other 2.118 r_angle_refined_deg 0.734 r_angle_other_deg 0.266 r_nbd_refined 0.193 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.123 r_nbd_other 0.1 r_symmetry_nbtor_other 0.079 r_symmetry_nbd_refined 0.075 r_symmetry_xyhbond_nbd_refined 0.056 r_chiral_restr 0.033 r_chiral_restr_other 0.024 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7440 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing