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Crystal structure of S-adenosyl-L-homocysteine hydrolase treated at 368 K from Pyrococcus furiosus in complex with inosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7R37
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 Before crystallization, enzyme was heat treated at 95 degree celsius (or 368 Kelvin).
26% (w/v) PEG 1500 with 100 mM MMT, pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.93 36.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.714 α = 90 b = 111.714 β = 90 c = 122.11 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 2023-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.28022 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.033 48.31 99.71 0.2373 0.0466 0.99 15.36 26.8 50113 33.14
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 2.033 2.106 0.681
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-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.033 48.308 50111 2507 99.749 0.157 0.1547 0.2032 0.1882 34.257
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] 0.03 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.95 r_dihedral_angle_6_deg 15.093 r_dihedral_angle_2_deg 10.418 r_lrange_it 7.67 r_lrange_other 7.668 r_dihedral_angle_1_deg 6.452 r_scangle_it 6.423 r_scangle_other 6.423 r_scbond_it 4.218 r_scbond_other 4.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.95 r_dihedral_angle_6_deg 15.093 r_dihedral_angle_2_deg 10.418 r_lrange_it 7.67 r_lrange_other 7.668 r_dihedral_angle_1_deg 6.452 r_scangle_it 6.423 r_scangle_other 6.423 r_scbond_it 4.218 r_scbond_other 4.218 r_mcangle_it 3.392 r_mcangle_other 3.392 r_mcbond_it 2.452 r_mcbond_other 2.45 r_angle_refined_deg 1.425 r_angle_other_deg 0.467 r_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.176 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.16 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_1 0.074 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_dihedral_angle_other_2_deg 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6648 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling AutoSol phasing