5HXZ

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 5HXU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293Protein was at 15 mg/mL; reservoir was 2.5 M ammonium sulfate, 0.1 M bis-tris at pH 6.5; vapor diffusion sitting drops of 150 nL plus 150 nL; done at 20 C.
Crystal Properties
Matthews coefficientSolvent content
2.3848.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.63α = 90
b = 83.732β = 90
c = 215.102γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-03-30MSINGLE 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
12.3645.399.987.461689
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.362.4298.62.67.3

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 REPLACEMENTTHROUGHOUT5hxu2.3645.358648296399.870.225780.224280.25516RANDOM31.438
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]
0.570.83-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.62
r_dihedral_angle_4_deg16.102
r_dihedral_angle_3_deg14.78
r_long_range_B_refined6.61
r_long_range_B_other6.61
r_scangle_other6.066
r_dihedral_angle_1_deg5.389
r_scbond_it4.934
r_scbond_other4.932
r_mcangle_it4.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.62
r_dihedral_angle_4_deg16.102
r_dihedral_angle_3_deg14.78
r_long_range_B_refined6.61
r_long_range_B_other6.61
r_scangle_other6.066
r_dihedral_angle_1_deg5.389
r_scbond_it4.934
r_scbond_other4.932
r_mcangle_it4.658
r_mcangle_other4.658
r_mcbond_it3.729
r_mcbond_other3.728
r_angle_other_deg3.649
r_angle_refined_deg1.136
r_chiral_restr0.038
r_bond_refined_d0.006
r_gen_planes_other0.004
r_gen_planes_refined0.003
r_bond_other_d
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 Atoms10839
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing