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cyclic 2,3-diphosphoglycerate synthetase from the hyperthermophilic archaeon Methanothermus fervidus bound to 2,3-diphosphoglycerate and ADP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 8ORK ligand free
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 292.15 The substrate bound crystals grew in condition E12 of the Morpheus screen consisting of 0.12M Ethylene glycols mix, 0.1M Buffer System 3 pH 8.5 and 37.5% v/v of Precipitant Mix 4. where the different solution are:
Ethylene glycols mix: 0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol.
Buffer system 3: Tris (base); BICINE pH 8.5
Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.46 50.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.234 α = 97.015 b = 71.478 β = 103.424 c = 103.543 γ = 99.045
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 EIGER2 XE 16M 2020-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.23 69.92 97.7 0.081 0.115 0.986 6.3 1.8 92153
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 2.23 2.27 97 0.382 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.23 69.92 92153 85.28 0.216 0.256 0.2189
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 14232 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 255
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing