6F3N

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with SAH in the presence of K+ and Zn2+ cations


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29250 mM KH2PO4, 20% (w/v) PEG8000, 1 mM S-adenosyl-L-homocysteine
Crystal Properties
Matthews coefficientSolvent content
2.2445

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.585α = 90
b = 99.275β = 101.9
c = 111.721γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252014-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.30.8950BESSY14.3

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
11.852598.30.08210.22.2152489-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.92

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.8524.82150603148597.890.151360.151110.17648RANDOM20.83
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]
-0.31-0.170.040.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.654
r_dihedral_angle_4_deg14.142
r_dihedral_angle_3_deg12.851
r_dihedral_angle_1_deg6.326
r_long_range_B_refined3.778
r_long_range_B_other3.555
r_angle_refined_deg1.599
r_scangle_other1.273
r_angle_other_deg0.962
r_mcangle_it0.889
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.654
r_dihedral_angle_4_deg14.142
r_dihedral_angle_3_deg12.851
r_dihedral_angle_1_deg6.326
r_long_range_B_refined3.778
r_long_range_B_other3.555
r_angle_refined_deg1.599
r_scangle_other1.273
r_angle_other_deg0.962
r_mcangle_it0.889
r_mcangle_other0.889
r_scbond_it0.806
r_scbond_other0.806
r_mcbond_other0.566
r_mcbond_it0.565
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.007
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14196
Nucleic Acid Atoms
Solvent Atoms1611
Heterogen Atoms286

Software

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