8JM6

Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A/S333V/P340L from Prunus communis complexed with 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde (catalytic conformation)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LR8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5291tris-bicine, 100 mM, pH 8.5; CaCl2, 60 mM; MgCl2, 60 mM; PEG 500MME, 20%, v/v; PEG 20000, 10%, w/v
Crystal Properties
Matthews coefficientSolvent content
2.5251.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.596α = 90
b = 90.682β = 90
c = 130.512γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97854SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.9501000.1890.1960.0540.9933.41345993
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.931000.9771.0170.2820.8812.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9146.442732221397.060.1490.14910.147350.18367RANDOM20.958
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]
0.16-0.20.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.657
r_dihedral_angle_4_deg16.533
r_dihedral_angle_3_deg12.175
r_dihedral_angle_1_deg7.776
r_long_range_B_refined5.638
r_long_range_B_other5.328
r_scangle_other4.062
r_scbond_it2.71
r_scbond_other2.685
r_mcangle_it2.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.657
r_dihedral_angle_4_deg16.533
r_dihedral_angle_3_deg12.175
r_dihedral_angle_1_deg7.776
r_long_range_B_refined5.638
r_long_range_B_other5.328
r_scangle_other4.062
r_scbond_it2.71
r_scbond_other2.685
r_mcangle_it2.49
r_mcangle_other2.49
r_mcbond_it1.767
r_mcbond_other1.764
r_angle_refined_deg1.725
r_angle_other_deg1.442
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3960
Nucleic Acid Atoms
Solvent Atoms480
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
HKL-3000data reduction
REFMACphasing