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Crystal structure of a member of the VapBC family of toxin-antitoxin systems, VapBC-5, from Mycobacterium tuberculosis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 30% MPD, 0.1 M Na acetate pH 4.6, 0.2 M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 1.89 34.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.83 α = 90 b = 64.83 β = 90 c = 164.65 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 77 CCD ADSC QUANTUM 315 2007-12-21 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 315 2007-12-21 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9795 ALS 8.2.2 2 SYNCHROTRON APS BEAMLINE 24-ID-C 1.5418 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.76 56.17 0.058 11.8 9.1 19839
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.76 1.86 0.409 2.49 2.9 957
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.76 56.17 16830 915 84.53 0.21448 0.21276 0.2115 0.24709 0.2456 RANDOM 21.009
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] 0.17 0.08 0.17 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.5 r_dihedral_angle_4_deg 15.088 r_dihedral_angle_3_deg 14.965 r_dihedral_angle_1_deg 4.969 r_scangle_it 3.186 r_scbond_it 1.995 r_mcangle_it 1.399 r_angle_refined_deg 1.282 r_mcbond_it 0.801 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.5 r_dihedral_angle_4_deg 15.088 r_dihedral_angle_3_deg 14.965 r_dihedral_angle_1_deg 4.969 r_scangle_it 3.186 r_scbond_it 1.995 r_mcangle_it 1.399 r_angle_refined_deg 1.282 r_mcbond_it 0.801 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1206 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling SHELXD phasing