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Engineered glycolyl-CoA reductase comprising 8 mutations with bound NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 288 Enzyme (6.5 mg/mL) was mixed with 0.2 M potassium citrate/KOH pH 8.4, 20% (w/v) PEG 3350, and supplemented with NADP+ from a 30 mM stock in a ratio of 2:2:1 (enzyme: crystallization buffer: substrate). The final drop volume was 5 micro liters.
Crystal Properties Matthews coefficient Solvent content 3.69 66.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 362.202 α = 90 b = 123.183 β = 109.25 c = 165.096 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 6M 2018-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976251 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.579 39.133 98.8 0.13 0.15 0.074 7.6 4 212592 212592 50.94
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) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.72 97.4 0.969 0.969 1.116 0.548 0.8 4.1
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 5JFL 2.579 39.133 1.34 410676 3860 96.77 0.1916 0.1915 0.1922 0.2098 0.21 58.0242
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 32970 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 470
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing