6F3Q

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with adenine and Rb+ cation


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29250 mM RbH2PO4, 20% (w/v) PEG8000, 2 mM 2'-deoxyadenosine
Crystal Properties
Matthews coefficientSolvent content
2.2445.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.492α = 90
b = 99.442β = 101.93
c = 111.714γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MSi-111 crystal2016-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.8077BESSY14.1

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
11.455098.60.04916.64318355-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.54

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 REPLACEMENTTHROUGHOUT6F3P1.4548.53315012334398.640.093250.092910.12443RANDOM16.59
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]
0.10.070.58-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.837
r_sphericity_free26.627
r_dihedral_angle_4_deg13.495
r_dihedral_angle_3_deg12.075
r_sphericity_bonded10.967
r_dihedral_angle_1_deg6.413
r_long_range_B_refined3.671
r_scangle_other3.503
r_rigid_bond_restr3.471
r_long_range_B_other3.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.837
r_sphericity_free26.627
r_dihedral_angle_4_deg13.495
r_dihedral_angle_3_deg12.075
r_sphericity_bonded10.967
r_dihedral_angle_1_deg6.413
r_long_range_B_refined3.671
r_scangle_other3.503
r_rigid_bond_restr3.471
r_long_range_B_other3.37
r_scbond_it3.005
r_scbond_other3.005
r_mcangle_it2.138
r_mcangle_other2.138
r_mcbond_it1.879
r_mcbond_other1.879
r_angle_refined_deg1.804
r_angle_other_deg1.046
r_chiral_restr0.122
r_bond_refined_d0.018
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 Atoms14196
Nucleic Acid Atoms
Solvent Atoms2128
Heterogen Atoms274

Software

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