8AJT

Crystal structure of the H323A 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 DROP293Morpheus Crystallization Screen, Condition C12
Crystal Properties
Matthews coefficientSolvent content
2.9958.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 176.71α = 90
b = 134.561β = 105.713
c = 108.091γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.97625PETRA III, EMBL c/o DESYP13 (MX1)

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
11.4642.55998.90.9998.883.372826623
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)
11.461.550.3160.53

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-VALUE6F3M1.49942.559386964104599.8320.1520.15210.16730.664
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]
-1.015-0.809-0.6511.831
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.417
r_dihedral_angle_4_deg15.182
r_dihedral_angle_3_deg13.099
r_dihedral_angle_1_deg7.375
r_lrange_it5.702
r_lrange_other5.513
r_scangle_it3.466
r_scangle_other3.451
r_scbond_it2.409
r_scbond_other2.377
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.417
r_dihedral_angle_4_deg15.182
r_dihedral_angle_3_deg13.099
r_dihedral_angle_1_deg7.375
r_lrange_it5.702
r_lrange_other5.513
r_scangle_it3.466
r_scangle_other3.451
r_scbond_it2.409
r_scbond_other2.377
r_mcangle_it1.742
r_mcangle_other1.742
r_angle_refined_deg1.485
r_angle_other_deg1.433
r_mcbond_it1.281
r_mcbond_other1.27
r_symmetry_nbd_refined0.286
r_nbd_refined0.225
r_nbd_other0.219
r_symmetry_nbd_other0.182
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.145
r_symmetry_xyhbond_nbd_refined0.139
r_metal_ion_refined0.116
r_chiral_restr0.085
r_symmetry_nbtor_other0.082
r_ncsr_local_group_10.07
r_ncsr_local_group_40.066
r_symmetry_metal_ion_refined0.065
r_ncsr_local_group_60.064
r_ncsr_local_group_50.062
r_ncsr_local_group_30.058
r_ncsr_local_group_20.051
r_gen_planes_refined0.013
r_bond_refined_d0.011
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14188
Nucleic Acid Atoms
Solvent Atoms1575
Heterogen Atoms379

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing