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Sulfatase from Mycobacterium tuberculosis (Rv3406) in complex with N-oxalylglycine (NOG)
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 2.22 44.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.535 α = 90 b = 128.336 β = 90 c = 138.693 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 2021-03-23 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 2.64 47.676 99.2 0.03 0.999 11.9 13.5 34771
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.64 2.77 94.5 0.381 0.86 1.2 13.3
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 2.644 47.676 34635 1734 98.988 0.253 0.2502 0.2674 0.2995 0.3143 random selection 85.363
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] 13.329 -6.662 -6.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.598 r_dihedral_angle_6_deg 10.454 r_dihedral_angle_2_deg 8.221 r_dihedral_angle_1_deg 5.415 r_lrange_it 2.578 r_lrange_other 2.578 r_scbond_it 1.219 r_scbond_other 1.217 r_mcangle_it 1.212 r_mcangle_other 1.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.598 r_dihedral_angle_6_deg 10.454 r_dihedral_angle_2_deg 8.221 r_dihedral_angle_1_deg 5.415 r_lrange_it 2.578 r_lrange_other 2.578 r_scbond_it 1.219 r_scbond_other 1.217 r_mcangle_it 1.212 r_mcangle_other 1.212 r_scangle_it 1.187 r_scangle_other 1.187 r_mcbond_it 0.701 r_mcbond_other 0.7 r_angle_refined_deg 0.641 r_angle_other_deg 0.241 r_nbd_refined 0.172 r_symmetry_nbd_other 0.165 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.113 r_xyhbond_nbd_refined 0.103 r_nbd_other 0.092 r_symmetry_nbd_refined 0.084 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.029 r_chiral_restr_other 0.021 r_bond_refined_d 0.002 r_gen_planes_refined 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 7227 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing