5HXU

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 4BVQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9293Protein at 15 mg/mL; reservoir was 2.5 M ammonium sulfate with 10% (v/v) MMT buffer at pH 9; sitting drop setup with 150 nL plus 150 nL drops; crystals cryo-protected with AP/E core 150 basestock (Mobile 1, Australia).
Crystal Properties
Matthews coefficientSolvent content
2.4349.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.415α = 90
b = 83.415β = 90
c = 216.234γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX21.28221Australian 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
11.8345.798.122.226.667015
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.831.87813.520.5

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 REPLACEMENTTHROUGHOUT4bvq1.8341.562328321896.030.212680.210670.25165RANDOM25.162
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]
0.070.07-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.211
r_dihedral_angle_4_deg18.184
r_dihedral_angle_3_deg13.818
r_long_range_B_refined7.198
r_long_range_B_other7.105
r_scangle_other6.082
r_dihedral_angle_1_deg5.864
r_scbond_it4.327
r_scbond_other4.314
r_mcangle_it3.967
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.211
r_dihedral_angle_4_deg18.184
r_dihedral_angle_3_deg13.818
r_long_range_B_refined7.198
r_long_range_B_other7.105
r_scangle_other6.082
r_dihedral_angle_1_deg5.864
r_scbond_it4.327
r_scbond_other4.314
r_mcangle_it3.967
r_mcangle_other3.967
r_mcbond_it3.109
r_mcbond_other3.109
r_angle_refined_deg1.729
r_angle_other_deg1.594
r_chiral_restr0.106
r_bond_refined_d0.017
r_bond_other_d0.01
r_gen_planes_refined0.01
r_gen_planes_other0.007
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 Atoms5432
Nucleic Acid Atoms
Solvent Atoms617
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing