8AJU

Crystal structure of the Q65A mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29350 mM KH2PO4, 20% (w/v) PEG8000, 20% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
2.7955.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.132α = 90
b = 85.925β = 131.184
c = 125.568γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 2M2019-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918400BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.64541.67998.80.9957.573.764136460
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7495.90.5431.14

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6F3M1.64541.679136459210199.1150.1670.16650.198330.907
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]
-0.6350.0340.0570.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.264
r_dihedral_angle_4_deg14.857
r_dihedral_angle_3_deg13.082
r_dihedral_angle_1_deg7.358
r_lrange_it4.828
r_lrange_other4.235
r_scangle_it2.786
r_scangle_other2.786
r_scbond_it2.033
r_scbond_other2.033
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.264
r_dihedral_angle_4_deg14.857
r_dihedral_angle_3_deg13.082
r_dihedral_angle_1_deg7.358
r_lrange_it4.828
r_lrange_other4.235
r_scangle_it2.786
r_scangle_other2.786
r_scbond_it2.033
r_scbond_other2.033
r_mcangle_it1.926
r_mcangle_other1.926
r_angle_refined_deg1.629
r_mcbond_it1.482
r_mcbond_other1.482
r_angle_other_deg1.466
r_nbd_refined0.217
r_symmetry_xyhbond_nbd_refined0.199
r_symmetry_nbd_other0.181
r_xyhbond_nbd_refined0.171
r_nbtor_refined0.168
r_nbd_other0.167
r_symmetry_nbd_refined0.121
r_chiral_restr0.091
r_symmetry_nbtor_other0.082
r_ncsr_local_group_10.058
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7088
Nucleic Acid Atoms
Solvent Atoms1119
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing