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Crystal structure of Mycobacterium tuberculosis VapBC11 toxin-antitoxin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 293 0.1M Ammonium Sulphate, 0.3M Sodium formate, 0.1 Sodium cacodylate, 3 % w/v PGA-LM, 30% PEG400 (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.555 α = 90 b = 127.007 β = 90 c = 151.207 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M-F 2017-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0723 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.67 97.252 99.7 0.044 0.05 0.023 15.7 4.6 113379 113379
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.76 98.8 0.881 0.881 0.999 0.461 0.9 4.4
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 4CHG 1.67 97.25 107637 5653 99.57 0.1843 0.183 0.2086 0.2095 RANDOM 39.158
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] 0.52 0.11 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.146 r_sphericity_free 30.73 r_dihedral_angle_4_deg 15.315 r_rigid_bond_restr 13.195 r_dihedral_angle_3_deg 12.745 r_sphericity_bonded 12.625 r_dihedral_angle_1_deg 5.378 r_angle_refined_deg 1.298 r_angle_other_deg 0.78 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.146 r_sphericity_free 30.73 r_dihedral_angle_4_deg 15.315 r_rigid_bond_restr 13.195 r_dihedral_angle_3_deg 12.745 r_sphericity_bonded 12.625 r_dihedral_angle_1_deg 5.378 r_angle_refined_deg 1.298 r_angle_other_deg 0.78 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6122 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing