5HY4

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 concentrated to 4.2 mg/mL; reservoir was 20% PEG 3350 and 0.2 M magnesium acetate at 8 C; drops were 150 nL protein plus 150 nL reservoir.
Crystal Properties
Matthews coefficientSolvent content
2.143.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.762α = 90
b = 105.799β = 90
c = 299.127γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95370Australian 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
12.5646.799.512.57.595206
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.562.698.91.87.6

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 REPLACEMENTTHROUGHOUT5HY02.5646.790462466699.380.23110.229430.26343RANDOM53.899
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]
-0.58-1.371.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.808
r_dihedral_angle_4_deg19.431
r_dihedral_angle_3_deg14.658
r_long_range_B_other11.375
r_long_range_B_refined11.373
r_dihedral_angle_1_deg7.244
r_mcangle_it6.846
r_mcangle_other6.846
r_scangle_other6.243
r_mcbond_it4.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.808
r_dihedral_angle_4_deg19.431
r_dihedral_angle_3_deg14.658
r_long_range_B_other11.375
r_long_range_B_refined11.373
r_dihedral_angle_1_deg7.244
r_mcangle_it6.846
r_mcangle_other6.846
r_scangle_other6.243
r_mcbond_it4.378
r_mcbond_other4.377
r_scbond_it3.923
r_scbond_other3.923
r_angle_other_deg2.097
r_angle_refined_deg1.522
r_chiral_restr0.081
r_bond_refined_d0.013
r_bond_other_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.009
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 Atoms19446
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing