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Crystal structure of the Q65N 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 2.41 48.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.503 α = 90 b = 133.618 β = 103.18 c = 100.865 γ = 90
Symmetry Space Group P 1 21 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 2021-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 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 1.819 79.133 99.7 0.097 0.999 12.05 6.87 171257
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.819 1.917 0.144 0.156 0.683 1.11
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6F3M 1.819 79.133 171243 1285 99.703 0.16 0.1596 0.1941 0.2031 36.188
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] -1.157 -2.189 2.397 -0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.748 r_dihedral_angle_4_deg 15.589 r_dihedral_angle_3_deg 14.355 r_dihedral_angle_1_deg 7.558 r_lrange_it 4.908 r_lrange_other 4.771 r_scangle_it 2.811 r_scangle_other 2.783 r_scbond_it 1.919 r_scbond_other 1.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.748 r_dihedral_angle_4_deg 15.589 r_dihedral_angle_3_deg 14.355 r_dihedral_angle_1_deg 7.558 r_lrange_it 4.908 r_lrange_other 4.771 r_scangle_it 2.811 r_scangle_other 2.783 r_scbond_it 1.919 r_scbond_other 1.894 r_mcangle_it 1.872 r_mcangle_other 1.872 r_angle_refined_deg 1.378 r_angle_other_deg 1.35 r_mcbond_it 1.326 r_mcbond_other 1.326 r_nbd_other 0.317 r_symmetry_nbd_refined 0.291 r_nbd_refined 0.213 r_symmetry_nbd_other 0.184 r_symmetry_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_other 0.118 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.078 r_ncsr_local_group_3 0.067 r_ncsr_local_group_5 0.067 r_ncsr_local_group_6 0.067 r_ncsr_local_group_1 0.066 r_ncsr_local_group_2 0.066 r_ncsr_local_group_4 0.066 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14224 Nucleic Acid Atoms Solvent Atoms 1324 Heterogen Atoms 279
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing