6KFA

Hydroxynitrile lyase from the millipede, Chamberlinius hualienensis bound with acetate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52930.2 M ammonium sulfate, 0.1 M sodium acetate (pH 5.0), 28-32% (w/v) PEG monomethyl ether 2000, 0.3 M NDSB-195
Crystal Properties
Matthews coefficientSolvent content
3.0659.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.247α = 90
b = 58.247β = 90
c = 224.978γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.00Photon FactoryBL-1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.550.441000.04626.510.435572
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.691000.2290.2510.2290.0730.9899.511.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.550.4435572184399.970.174560.173920.18686RANDOM18.32
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]
0.440.220.44-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.766
r_dihedral_angle_3_deg12.015
r_dihedral_angle_4_deg11.068
r_dihedral_angle_1_deg6.716
r_long_range_B_refined4.854
r_long_range_B_other4.403
r_scangle_other1.964
r_angle_refined_deg1.256
r_scbond_it1.221
r_scbond_other1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.766
r_dihedral_angle_3_deg12.015
r_dihedral_angle_4_deg11.068
r_dihedral_angle_1_deg6.716
r_long_range_B_refined4.854
r_long_range_B_other4.403
r_scangle_other1.964
r_angle_refined_deg1.256
r_scbond_it1.221
r_scbond_other1.22
r_mcangle_it1.146
r_mcangle_other1.146
r_angle_other_deg0.903
r_mcbond_it0.705
r_mcbond_other0.705
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1280
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELXCDphasing