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Crystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclipostin-like inhibitor CyC17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 MES Na 0.1 M
NH4SO4 1.656 M
PEG400 6.88%
Crystal Properties Matthews coefficient Solvent content 2.7 54.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.958 α = 90 b = 87.404 β = 90 c = 106.128 γ = 90
Symmetry Space Group P 2 2 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 9M 2021-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980114 SOLEIL PROXIMA 2
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 1.81 45.36 99.8 0.118 0.122 0.033 0.999 16.5 13.4 66020 19.116
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 1.81 1.85 96 1.39 1.449 0.404 0.638 12.4
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 (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 7ZJT 1.81 45.36 62617 3372 99.74 0.1839 0.1823 0.1915 0.2132 0.2211 RANDOM 26.724
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] -0.5 0.92 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.46 r_dihedral_angle_4_deg 16.217 r_dihedral_angle_3_deg 12.625 r_dihedral_angle_1_deg 6.736 r_angle_refined_deg 1.517 r_angle_other_deg 1.363 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.46 r_dihedral_angle_4_deg 16.217 r_dihedral_angle_3_deg 12.625 r_dihedral_angle_1_deg 6.736 r_angle_refined_deg 1.517 r_angle_other_deg 1.363 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4388 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 20
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing