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Crystal structure of the Q65A 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 2.79 55.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.132 α = 90 b = 85.925 β = 131.184 c = 125.568 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 PILATUS3 S 2M 2019-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918400 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.645 41.679 98.8 0.995 7.57 3.764 136460
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 1.65 1.74 95.9 0.543 1.14
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 1.645 41.679 136459 2101 99.115 0.167 0.1665 0.177 0.1983 0.2058 30.907
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] -0.635 0.034 0.057 0.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.264 r_dihedral_angle_4_deg 14.857 r_dihedral_angle_3_deg 13.082 r_dihedral_angle_1_deg 7.358 r_lrange_it 4.828 r_lrange_other 4.235 r_scangle_it 2.786 r_scangle_other 2.786 r_scbond_it 2.033 r_scbond_other 2.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.264 r_dihedral_angle_4_deg 14.857 r_dihedral_angle_3_deg 13.082 r_dihedral_angle_1_deg 7.358 r_lrange_it 4.828 r_lrange_other 4.235 r_scangle_it 2.786 r_scangle_other 2.786 r_scbond_it 2.033 r_scbond_other 2.033 r_mcangle_it 1.926 r_mcangle_other 1.926 r_angle_refined_deg 1.629 r_mcbond_it 1.482 r_mcbond_other 1.482 r_angle_other_deg 1.466 r_nbd_refined 0.217 r_symmetry_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.181 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.168 r_nbd_other 0.167 r_symmetry_nbd_refined 0.121 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_1 0.058 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7088 Nucleic Acid Atoms Solvent Atoms 1119 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing