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Crystal structure of Mycobacterium tuberculosis ArgB in complex with methyl 4-hydroxy-3-iodobenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9.5 291 1260 mM ammonium sulphate
100 mM CHES pH 9.5
200 mM NaCl
Crystal Properties Matthews coefficient Solvent content 3.37 63.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.238 α = 90 b = 174.238 β = 90 c = 72.03 γ = 120
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 2016-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.648 87.12 100 0.076 0.08 0.025 0.999 20.3 10.1 12283 73.1
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 2.65 2.79 100 1.27 1.336 0.413 0.759 10.4
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 THROUGHOUT 2AP9 2.648 52.099 1.36 12277 610 99.97 0.1961 0.193 0.2041 0.2552 0.2572 84.3743
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 17.429 f_angle_d 1.093 f_chiral_restr 0.061 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2126 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction Coot model building