6F3M

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa complexed with adenosine, K+ and Zn2+ cations


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6F3P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29250 mM KH2PO4, 20 % (W/V) PEG8000, 2 mM adenosine
Crystal Properties
Matthews coefficientSolvent content
2.3948.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.976α = 90
b = 104.145β = 100.71
c = 107.634γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252013-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

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
11.65097.80.06114.93.2244909-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.69

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 REPLACEMENTTHROUGHOUT6F3P1.648.7242459245097.810.15120.150970.17421RANDOM26.431
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]
0.180.570.03-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.46
r_dihedral_angle_3_deg11.949
r_dihedral_angle_4_deg11.793
r_dihedral_angle_1_deg6.421
r_long_range_B_refined4.373
r_long_range_B_other4.096
r_scangle_other1.94
r_angle_refined_deg1.58
r_scbond_it1.3
r_scbond_other1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.46
r_dihedral_angle_3_deg11.949
r_dihedral_angle_4_deg11.793
r_dihedral_angle_1_deg6.421
r_long_range_B_refined4.373
r_long_range_B_other4.096
r_scangle_other1.94
r_angle_refined_deg1.58
r_scbond_it1.3
r_scbond_other1.3
r_mcangle_it1.134
r_mcangle_other1.134
r_angle_other_deg0.975
r_mcbond_it0.808
r_mcbond_other0.808
r_chiral_restr0.1
r_bond_refined_d0.013
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 Atoms1975
Heterogen Atoms298

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
ARP/wARPmodel building