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X-ray crystal structure of the formyltransferase/hydrolase complex (FhcABCD) from Methylorubrum extorquens in complex with methylofuran
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 292 The best hit was obtained in a CombiClover Junior Plate by using the sitting drop vapor diffusion method. 2 ul protein was mixed with 1 ul of the crystallization solution containing 0.2 M CaCl2 and 20% (w/v) PEG 3350. The protein buffer contained 25 mM Tris pH 7.7, 10% (v/v) glycerol, 2 mM DTT, 6 mM KCl and 200 mM NaCl.
Crystal Properties Matthews coefficient Solvent content 2.99 58.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.974 α = 84.97 b = 130.322 β = 75.91 c = 172.689 γ = 82.09
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 2016-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00005 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.1 48.5 96.6 0.149 0.149 0.209 0.147 0.983 5.2 1.8 124496
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.27 96.9 1.286 1.286 1.811 1.275 0.308 0.6 1.8
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 5T5I 3.1 24.949 1.96 123826 5953 96.22 0.2227 0.2212 0.2239 0.2513 0.2226 108.4772
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 43018 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 270
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing