5HY2

Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HY0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5281Protein was at 2.7 mg/mL with added atrazine; reservoir was 22% PEG 3350, 86 mM sodium acetate; drops were 150 nL protein plus 140 nL reservoir plus 10 nL microseeds.
Crystal Properties
Matthews coefficientSolvent content
2.6854.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.297α = 90
b = 72.75β = 92.22
c = 133.054γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.97070Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.646.699.9147.527567
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.7299.12.17.4

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 REPLACEMENTTHROUGHOUT5HY02.641.526209135499.850.204030.202170.24123RANDOM54.402
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]
-0.94-1.974.35-3.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.997
r_dihedral_angle_4_deg20.962
r_dihedral_angle_3_deg15.888
r_long_range_B_other11.565
r_long_range_B_refined11.564
r_scangle_other7.241
r_mcangle_it7.203
r_mcangle_other7.203
r_dihedral_angle_1_deg5.841
r_scbond_it4.644
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.997
r_dihedral_angle_4_deg20.962
r_dihedral_angle_3_deg15.888
r_long_range_B_other11.565
r_long_range_B_refined11.564
r_scangle_other7.241
r_mcangle_it7.203
r_mcangle_other7.203
r_dihedral_angle_1_deg5.841
r_scbond_it4.644
r_scbond_other4.643
r_mcbond_it4.59
r_mcbond_other4.587
r_angle_other_deg1.474
r_angle_refined_deg1.259
r_chiral_restr0.067
r_bond_refined_d0.01
r_bond_other_d0.01
r_gen_planes_refined0.007
r_gen_planes_other0.006
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4719
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing