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Crystal structure of the H323A 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 Morpheus Crystallization Screen, Condition C12
Crystal Properties Matthews coefficient Solvent content 2.99 58.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.71 α = 90 b = 134.561 β = 105.713 c = 108.091 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 2021-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97625 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.46 42.559 98.9 0.999 8.88 3.372 826623
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 1.46 1.55 0.316 0.53
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 1.499 42.559 386964 1045 99.832 0.152 0.1521 0.1521 0.167 0.1672 30.664
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] -1.015 -0.809 -0.651 1.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.417 r_dihedral_angle_4_deg 15.182 r_dihedral_angle_3_deg 13.099 r_dihedral_angle_1_deg 7.375 r_lrange_it 5.702 r_lrange_other 5.513 r_scangle_it 3.466 r_scangle_other 3.451 r_scbond_it 2.409 r_scbond_other 2.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.417 r_dihedral_angle_4_deg 15.182 r_dihedral_angle_3_deg 13.099 r_dihedral_angle_1_deg 7.375 r_lrange_it 5.702 r_lrange_other 5.513 r_scangle_it 3.466 r_scangle_other 3.451 r_scbond_it 2.409 r_scbond_other 2.377 r_mcangle_it 1.742 r_mcangle_other 1.742 r_angle_refined_deg 1.485 r_angle_other_deg 1.433 r_mcbond_it 1.281 r_mcbond_other 1.27 r_symmetry_nbd_refined 0.286 r_nbd_refined 0.225 r_nbd_other 0.219 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.139 r_metal_ion_refined 0.116 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_1 0.07 r_ncsr_local_group_4 0.066 r_symmetry_metal_ion_refined 0.065 r_ncsr_local_group_6 0.064 r_ncsr_local_group_5 0.062 r_ncsr_local_group_3 0.058 r_ncsr_local_group_2 0.051 r_gen_planes_refined 0.013 r_bond_refined_d 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14188 Nucleic Acid Atoms Solvent Atoms 1575 Heterogen Atoms 379
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing