8AJV

Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa crystallized 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
3.0759.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.481α = 90
b = 211.877β = 105.325
c = 111.351γ = 90
Symmetry
Space GroupP 1 21 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)0.9762PETRA 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
11.995.879990.9979.726.622453838
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)
11.91.950.593

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-VALUE6F3M1.995.879386694116399.2140.160.16040.193836.115
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]
-7.686-0.55417.862-10.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.917
r_dihedral_angle_4_deg16.942
r_dihedral_angle_3_deg14.256
r_dihedral_angle_1_deg7.822
r_lrange_it4.466
r_lrange_other4.466
r_scangle_it3.35
r_scangle_other3.35
r_scbond_it2.761
r_scbond_other2.761
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.917
r_dihedral_angle_4_deg16.942
r_dihedral_angle_3_deg14.256
r_dihedral_angle_1_deg7.822
r_lrange_it4.466
r_lrange_other4.466
r_scangle_it3.35
r_scangle_other3.35
r_scbond_it2.761
r_scbond_other2.761
r_mcangle_it2.717
r_mcangle_other2.717
r_mcbond_it2.422
r_mcbond_other2.422
r_angle_refined_deg1.53
r_angle_other_deg1.325
r_xyhbond_nbd_refined0.225
r_symmetry_xyhbond_nbd_refined0.206
r_nbd_refined0.204
r_symmetry_nbd_refined0.203
r_nbd_other0.192
r_symmetry_nbd_other0.181
r_nbtor_refined0.154
r_symmetry_xyhbond_nbd_other0.15
r_chiral_restr0.092
r_metal_ion_refined0.084
r_symmetry_nbtor_other0.079
r_ncsr_local_group_200.068
r_ncsr_local_group_190.066
r_ncsr_local_group_70.065
r_ncsr_local_group_270.064
r_ncsr_local_group_280.064
r_ncsr_local_group_30.063
r_ncsr_local_group_210.063
r_ncsr_local_group_230.063
r_ncsr_local_group_250.063
r_ncsr_local_group_50.062
r_ncsr_local_group_260.062
r_ncsr_local_group_160.061
r_ncsr_local_group_10.059
r_ncsr_local_group_180.059
r_ncsr_local_group_20.058
r_ncsr_local_group_130.058
r_ncsr_local_group_240.058
r_ncsr_local_group_60.057
r_ncsr_local_group_100.057
r_ncsr_local_group_120.057
r_ncsr_local_group_140.055
r_ncsr_local_group_40.054
r_ncsr_local_group_80.054
r_ncsr_local_group_90.054
r_ncsr_local_group_150.054
r_ncsr_local_group_220.052
r_ncsr_local_group_110.048
r_ncsr_local_group_170.046
r_gen_planes_refined0.014
r_bond_refined_d0.012
r_gen_planes_other0.002
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28408
Nucleic Acid Atoms
Solvent Atoms2820
Heterogen Atoms559

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing