8AGP

Halogenated product of limonene epoxide turnover by epoxide hydrolase from metagenomic source ch65


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH291Morpheus crystallisation kit condition C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000. The crystal was incubated with 1mM mixture of cis (1R,2S,4R) and trans (1S,2R,4R) isomers of (+)-limonene oxide for 1 hour 20 mins to produce a halogenated product in the active site.
Crystal Properties
Matthews coefficientSolvent content
2.0941.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.83α = 90
b = 46.11β = 98.41
c = 93γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4951.26399.10.9988.83.293810
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.520.366

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5ng71.4951.26393795470299.0670.180.17790.215626.938
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]
-0.91-0.9370.0141.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.286
r_dihedral_angle_4_deg20.713
r_dihedral_angle_3_deg14.396
r_lrange_it9.207
r_scangle_it8.754
r_scbond_it7.027
r_dihedral_angle_1_deg5.999
r_mcangle_it5.688
r_mcbond_it4.62
r_angle_refined_deg1.655
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.286
r_dihedral_angle_4_deg20.713
r_dihedral_angle_3_deg14.396
r_lrange_it9.207
r_scangle_it8.754
r_scbond_it7.027
r_dihedral_angle_1_deg5.999
r_mcangle_it5.688
r_mcbond_it4.62
r_angle_refined_deg1.655
r_nbtor_refined0.321
r_symmetry_nbd_refined0.256
r_nbd_refined0.225
r_symmetry_xyhbond_nbd_refined0.199
r_xyhbond_nbd_refined0.156
r_ncsr_local_group_10.123
r_chiral_restr0.116
r_bond_refined_d0.01
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4822
Nucleic Acid Atoms
Solvent Atoms432
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
BUSTERrefinement
PARROTphasing
Cootmodel building