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Catabolism of the Cholesterol Side Chain in Mycobacterium tuberculosis is Controlled by a Redox-Sensitive Thiol Switch
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M citrate, pH 5.5, 0.7 M (NH4)2HPO4, 0.3 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.54 51.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.289 α = 90 b = 120.289 β = 90 c = 206.03 γ = 120
Symmetry Space Group P 63 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 CCD RAYONIX MX-225 2012-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.19 46.17 100 0.1 15.2 9.8 46018
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.26 100 0.96 0.756 2.6 9.7
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 4UBW 2.19 46.17 43647 2320 99.91 0.1843 0.18213 0.1958 0.22568 0.2345 RANDOM 72.984
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] 0.72 0.36 0.72 -2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.149 r_dihedral_angle_3_deg 16.958 r_dihedral_angle_4_deg 16.128 r_long_range_B_refined 8.395 r_long_range_B_other 8.379 r_dihedral_angle_1_deg 6.534 r_scangle_other 5.824 r_mcangle_it 5.049 r_mcangle_other 5.049 r_scbond_it 3.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.149 r_dihedral_angle_3_deg 16.958 r_dihedral_angle_4_deg 16.128 r_long_range_B_refined 8.395 r_long_range_B_other 8.379 r_dihedral_angle_1_deg 6.534 r_scangle_other 5.824 r_mcangle_it 5.049 r_mcangle_other 5.049 r_scbond_it 3.906 r_scbond_other 3.905 r_mcbond_it 3.331 r_mcbond_other 3.328 r_angle_refined_deg 1.619 r_angle_other_deg 0.866 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5362 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing