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Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with inosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 comprising 26% (w/v) PEG 1500 with 100 mM MMT, pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.96 37.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.531 α = 90 b = 112.531 β = 90 c = 122.831 γ = 90
Symmetry Space Group P 42 21 2
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 EIGER X 16M 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.28 48.62 99.82 0.15 9.8 12.7 36380 40.35
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 2.28 2.41 0.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5axa 2.28 48.62 1.34 36319 1826 99.85 0.164 0.1613 0.1687 0.2159 0.2165 RANDOM 45.14
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.2497 f_angle_d 0.8501 f_chiral_restr 0.0514 f_bond_d 0.0069 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6648 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing