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Crystal structure of K449E variant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F3P 6f3p
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 50 mM KH2PO4, 16% PEG 8000, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.81 56.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.881 α = 90 b = 85.916 β = 122.08 c = 111.824 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 EIGER2 S 16M 2021-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.41 67.13 98.2 0.086 0.097 0.998 9.26 4.614 215913 26.146
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 1.41 1.5 96.7 2.121 2.398 0.302 0.82 4.611
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 (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 THROUGHOUT 6f3p 1.41 67.13 186719 1153 85.64 0.1673 0.1669 0.1671 0.2246 0.2244 RANDOM 16.762
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] -0.6 -0.01 -0.49 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.019 r_dihedral_angle_4_deg 18.769 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_1_deg 7.135 r_rigid_bond_restr 3.37 r_angle_refined_deg 1.824 r_angle_other_deg 1.528 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.019 r_dihedral_angle_4_deg 18.769 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_1_deg 7.135 r_rigid_bond_restr 3.37 r_angle_refined_deg 1.824 r_angle_other_deg 1.528 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7096 Nucleic Acid Atoms Solvent Atoms 1709 Heterogen Atoms 138
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing