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Crystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclophostin-like inhibitor CyC8b
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 5.76%
Crystal Properties Matthews coefficient Solvent content 2.69 54.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.834 α = 90 b = 87.187 β = 90 c = 105.914 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 EIGER2 X 9M 2021-07-28 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 2.2 45.26 100 0.157 0.165 0.048 0.998 12.4 11.4 36843 30.436
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 2.2 2.27 99.8 1.349 1.412 0.413 0.696 11.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7ZJT 2.2 45.26 34964 1853 99.89 0.1779 0.1754 0.2235 0.2101 RANDOM 36.045
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] -0.8 0.29 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.786 r_dihedral_angle_4_deg 16.408 r_dihedral_angle_3_deg 13.847 r_dihedral_angle_1_deg 7.071 r_angle_refined_deg 1.808 r_angle_other_deg 1.389 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.786 r_dihedral_angle_4_deg 16.408 r_dihedral_angle_3_deg 13.847 r_dihedral_angle_1_deg 7.071 r_angle_refined_deg 1.808 r_angle_other_deg 1.389 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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 108 Heterogen Atoms 35
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing