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Crystal structure of the F324A mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F3M 6F3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 50 mM KH2PO4, 20% (w/v) PEG8000, 20% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.05 59.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.844 α = 90 b = 134.962 β = 106.043 c = 109.393 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 EIGER X 16M 2021-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97625 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.68 105.921 99.6 0.064 0.998 11.76 5.319 280732
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 1.68 1.78 98.5 0.56 1.02
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6F3M 1.68 105.921 280727 1039 99.656 0.151 0.1509 0.163 0.1778 0.1884 39.342
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] -0.701 -0.384 -0.403 1.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.523 r_dihedral_angle_3_deg 13.459 r_dihedral_angle_4_deg 12.92 r_dihedral_angle_1_deg 7.456 r_lrange_it 5.799 r_lrange_other 5.586 r_scangle_it 4.066 r_scangle_other 4.066 r_scbond_it 2.789 r_scbond_other 2.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.523 r_dihedral_angle_3_deg 13.459 r_dihedral_angle_4_deg 12.92 r_dihedral_angle_1_deg 7.456 r_lrange_it 5.799 r_lrange_other 5.586 r_scangle_it 4.066 r_scangle_other 4.066 r_scbond_it 2.789 r_scbond_other 2.789 r_mcangle_it 2.09 r_mcangle_other 2.09 r_mcbond_it 1.606 r_mcbond_other 1.606 r_angle_other_deg 1.399 r_angle_refined_deg 1.382 r_symmetry_xyhbond_nbd_other 0.238 r_nbd_refined 0.221 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.157 r_nbd_other 0.135 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.076 r_symmetry_nbd_refined 0.076 r_metal_ion_refined 0.074 r_ncsr_local_group_3 0.063 r_ncsr_local_group_6 0.063 r_ncsr_local_group_5 0.059 r_ncsr_local_group_1 0.058 r_ncsr_local_group_2 0.058 r_ncsr_local_group_4 0.058 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14184 Nucleic Acid Atoms Solvent Atoms 1689 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing