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Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with adenine and Rb+ cation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 50 mM RbH2PO4, 20% (w/v) PEG8000, 2 mM 2'-deoxyadenosine
Crystal Properties Matthews coefficient Solvent content 2.24 45.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.492 α = 90 b = 99.442 β = 101.93 c = 111.714 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 PILATUS 6M Si-111 crystal 2016-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.8077 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 50 98.6 0.049 16.6 4 318355 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.54
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 1.45 48.53 315012 3343 98.64 0.09325 0.09291 0.0965 0.12443 0.1289 RANDOM 16.59
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] 0.1 0.07 0.58 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.837 r_sphericity_free 26.627 r_dihedral_angle_4_deg 13.495 r_dihedral_angle_3_deg 12.075 r_sphericity_bonded 10.967 r_dihedral_angle_1_deg 6.413 r_long_range_B_refined 3.671 r_scangle_other 3.503 r_rigid_bond_restr 3.471 r_long_range_B_other 3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.837 r_sphericity_free 26.627 r_dihedral_angle_4_deg 13.495 r_dihedral_angle_3_deg 12.075 r_sphericity_bonded 10.967 r_dihedral_angle_1_deg 6.413 r_long_range_B_refined 3.671 r_scangle_other 3.503 r_rigid_bond_restr 3.471 r_long_range_B_other 3.37 r_scbond_it 3.005 r_scbond_other 3.005 r_mcangle_it 2.138 r_mcangle_other 2.138 r_mcbond_it 1.879 r_mcbond_other 1.879 r_angle_refined_deg 1.804 r_angle_other_deg 1.046 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14196 Nucleic Acid Atoms Solvent Atoms 2128 Heterogen Atoms 274
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing ARP/wARP model building