5UE1

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase in complex with adenine from Vibrio fischeri ES114


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72900.2 M CaCl2, 0.1 M HEPES, 20% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.1943.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.642α = 90
b = 72.915β = 109.6
c = 57.563γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDberyllium lenses2016-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.143092.20.060.7933.24.4144464
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.141.1690.60.572.14

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3DP91.1430137008742892.090.130590.129110.15785RANDOM16.867
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]
-0.59-0.16-0.370.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.651
r_sphericity_free20.89
r_dihedral_angle_4_deg17.648
r_dihedral_angle_3_deg11.997
r_sphericity_bonded10.485
r_dihedral_angle_1_deg6.442
r_rigid_bond_restr4.966
r_long_range_B_refined4.021
r_long_range_B_other3.932
r_scangle_other2.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.651
r_sphericity_free20.89
r_dihedral_angle_4_deg17.648
r_dihedral_angle_3_deg11.997
r_sphericity_bonded10.485
r_dihedral_angle_1_deg6.442
r_rigid_bond_restr4.966
r_long_range_B_refined4.021
r_long_range_B_other3.932
r_scangle_other2.86
r_scbond_it2.573
r_scbond_other2.569
r_angle_refined_deg2.002
r_mcangle_it1.607
r_mcangle_other1.607
r_mcbond_it1.299
r_mcbond_other1.296
r_angle_other_deg1.116
r_chiral_restr0.289
r_bond_refined_d0.02
r_gen_planes_refined0.01
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 Atoms3463
Nucleic Acid Atoms
Solvent Atoms682
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing