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Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NP8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293.15 Fsr from Methanothermococcus thermolithotrophicus was crystallized anaerobically under yellow light at a concentration of 11 mg ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol, 0.5 mM FAD and 0.0155 mM F420H2. 0.6 ul of sample was mixed with 0.6 ul reservoir solution. The reservoir solution contained 0.2 M Lithium sulfate, 0.1 M Bis-Tris, pH 5.5 and 25 % w/v Polyethylene glycol 3350. Crystals appeared after few days.
Crystal Properties Matthews coefficient Solvent content 2.98 58.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.148 α = 102.28 b = 124.157 β = 95.71 c = 241.062 γ = 90.25
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 2M-F 2020-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00004 SLS X06DA
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 1.55 121.276 94.5 0.183 0.198 0.075 0.996 8.7 7 1396397
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 1.55 1.689 70.9 1.623 1.755 0.664 0.439 1.5 6.9
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 7NP8 1.55 77.29 1.96 1396186 69210 75.51 0.1594 0.1588 0.1642 0.1711 0.175 26.3738
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 77290 Nucleic Acid Atoms Solvent Atoms 10774 Heterogen Atoms 3554
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling PHASER phasing