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Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with 3'-deoxyadenosine and K+ cation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 50 mM KH2PO4, 15% (W/V) PEG8000, 20%
(V/V) GLYCEROL, 2 mM 3'-deoxyadenosine
Crystal Properties Matthews coefficient Solvent content 2.81 56.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.9 α = 90 b = 85.74 β = 122.2 c = 112.01 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 CCD MARMOSAIC 300 mm CCD 2012-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 1.35 30 98.6 0.066 13.1 2.9 245319 -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 1.35 1.4
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 1LI4 1.35 30 244097 1220 97.66 0.10088 0.10075 0.1045 0.12701 0.1294 RANDOM 18.554
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] -0.54 0.18 0.45 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.619 r_sphericity_free 28.792 r_dihedral_angle_4_deg 13.492 r_dihedral_angle_3_deg 12.128 r_sphericity_bonded 10.376 r_dihedral_angle_1_deg 6.358 r_long_range_B_refined 3.599 r_long_range_B_other 3.191 r_rigid_bond_restr 3.063 r_scangle_other 3.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.619 r_sphericity_free 28.792 r_dihedral_angle_4_deg 13.492 r_dihedral_angle_3_deg 12.128 r_sphericity_bonded 10.376 r_dihedral_angle_1_deg 6.358 r_long_range_B_refined 3.599 r_long_range_B_other 3.191 r_rigid_bond_restr 3.063 r_scangle_other 3.031 r_scbond_other 2.562 r_scbond_it 2.56 r_mcangle_it 2.209 r_mcangle_other 2.209 r_mcbond_it 1.776 r_mcbond_other 1.776 r_angle_refined_deg 1.767 r_angle_other_deg 1.04 r_chiral_restr 0.126 r_bond_refined_d 0.016 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 7096 Nucleic Acid Atoms Solvent Atoms 1127 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing ARP/wARP model building