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Structure of GntC, a PLP-dependent enzyme catalyzing L-enduracididine biosynthesis from (S)-4-hydroxy-L-arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 283 19% (w/v) PEG 3350, 0.50 M MgCl2, 0.10 M Tris pH 8.5, and 1 mM PLP
Crystal Properties Matthews coefficient Solvent content 2.1 41.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.855 α = 90 b = 158.159 β = 90.01 c = 73.231 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 CCD ADSC QUANTUM 315r 2018-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.99992 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 73.23 93.1 0.115 10.9 5.2 75093
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.106 0.5725
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3OP7 2.1 73.23 1.41 75048 3660 93.09 0.2211 0.22 0.2417 0.2473 32.7388
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 11068 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction AutoProcess data reduction AutoProcess data scaling AutoProcess phasing