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Crystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal 5'-phosphate and 3-hydroxy-2-naphthoic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ADB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1 M Bis-Tris Propane pH 8.5
18% PEG Smear High (PEGs 6K, 8K, 10K)
0.2 M ammonium nitrate
10 mM nickel chloride
Crystal Properties Matthews coefficient Solvent content 2.5 50.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.19 α = 90 b = 184.35 β = 106.21 c = 71.3 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 100 PIXEL DECTRIS PILATUS 6M-F 2019-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.47 68.47 97.4 0.043 0.048 0.021 0.999 16.5 4.5 265823
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 1.47 1.51 86.7 0.812 0.987 0.547 0.5 3
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 4ADB 1.47 68.465 1.35 265761 13042 97.37 0.1778 0.1769 0.1803 0.1959 0.1958 24.1684
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11344 Nucleic Acid Atoms Solvent Atoms 1427 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction Coot model building