6F3P

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with 3'-deoxyadenosine and K+ cation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LI4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29250 mM KH2PO4, 15% (W/V) PEG8000, 20% (V/V) GLYCEROL, 2 mM 3'-deoxyadenosine
Crystal Properties
Matthews coefficientSolvent content
2.8156.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.9α = 90
b = 85.74β = 122.2
c = 112.01γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.353098.60.06613.12.9245319-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1LI41.3530244097122097.660.100880.100750.12701RANDOM18.554
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]
-0.540.180.45-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.619
r_sphericity_free28.792
r_dihedral_angle_4_deg13.492
r_dihedral_angle_3_deg12.128
r_sphericity_bonded10.376
r_dihedral_angle_1_deg6.358
r_long_range_B_refined3.599
r_long_range_B_other3.191
r_rigid_bond_restr3.063
r_scangle_other3.031
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.619
r_sphericity_free28.792
r_dihedral_angle_4_deg13.492
r_dihedral_angle_3_deg12.128
r_sphericity_bonded10.376
r_dihedral_angle_1_deg6.358
r_long_range_B_refined3.599
r_long_range_B_other3.191
r_rigid_bond_restr3.063
r_scangle_other3.031
r_scbond_other2.562
r_scbond_it2.56
r_mcangle_it2.209
r_mcangle_other2.209
r_mcbond_it1.776
r_mcbond_other1.776
r_angle_refined_deg1.767
r_angle_other_deg1.04
r_chiral_restr0.126
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms7096
Nucleic Acid Atoms
Solvent Atoms1127
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
ARP/wARPmodel building