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Crystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadBD from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RLJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 285 0,1 M NaCacodylate pH 6,5, 40% MPD and 5% PEG 8k
Crystal Properties Matthews coefficient Solvent content 2.84 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.646 α = 90 b = 96.646 β = 90 c = 143.921 γ = 120
Symmetry Space Group P 65 2 2
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 PILATUS 6M 2021-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 ALBA XALOC
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 1.892 83.698 94.7 0.056 0.057 0.014 0.999 27.3 18.6 14207 43.4800802836
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 1.892 2.216 75.6 1.247 1.112 0.287 0.942 2.4 14.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.00196723217 54.5657301655 1.36415165716 14142 1415 51.5303891561 0.250484525568 0.246052592853 0.2586 0.290455304595 0.2967 67.9591451609
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.1916183076 f_angle_d 0.762080824045 f_chiral_restr 0.0300435654885 f_bond_d 0.00364914135636 f_plane_restr 0.00361342669357
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2147 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection PHENIX refinement autoPROC data processing STARANISO data scaling Coot model building XDS data reduction XDS data scaling PHASER phasing