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Crystal structure of S-adenosyl-L-homocysteine hydrolase from Mus musculus 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 8 295 180 mM sodium formate, pH 6.9, and 22%
PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.22 α = 90 b = 102.526 β = 90 c = 173.408 γ = 90
Symmetry Space Group I 2 2 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 EIGER2 X 16M 2018-11-18 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) 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 2.48 88.25 98.8 0.18 0.99 7.8 5.7 31056
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.52 0.97 0.66
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 (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 2.48 88.25 29460 1594 98.84 0.14936 0.14578 0.1458 0.21625 0.2163 RANDOM 38.969
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] 0.57 -2.36 1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.039 r_dihedral_angle_3_deg 19.353 r_dihedral_angle_4_deg 15.701 r_long_range_B_refined 7.264 r_dihedral_angle_1_deg 7.11 r_scbond_it 4.213 r_mcangle_it 3.863 r_mcbond_it 2.706 r_angle_refined_deg 1.568 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.039 r_dihedral_angle_3_deg 19.353 r_dihedral_angle_4_deg 15.701 r_long_range_B_refined 7.264 r_dihedral_angle_1_deg 7.11 r_scbond_it 4.213 r_mcangle_it 3.863 r_mcbond_it 2.706 r_angle_refined_deg 1.568 r_chiral_restr 0.111 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6642 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing