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Crystal structure of a bacterial toxin from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2N9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 6% v/v Tacsimate pH 6.0, 0.1M MES monohydrate pH 6.0, 25% w/v Polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.539 α = 90 b = 60.14 β = 107.847 c = 28.121 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315 2016-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
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 1.9 19.35 99 0.143 5.71 1.9 12018 33.1999350093
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 1.901 1.969 0.213 2.37
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2N9V 1.90057258182 19.342176936 1.35089351612 12018 1217 92.3396081444 0.208353516868 0.204580059947 0.2065 0.243715343531 0.2514 39.7739305669
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 18.9869712963 f_angle_d 0.676935499824 f_chiral_restr 0.0443426162544 f_plane_restr 0.00495905706375 f_bond_d 0.00485101942181
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 563 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing