6JHC

Hydroxynitrile lyase from the millipede, Chamberlinius hualienensis (ligand free)


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
3.0559.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.382α = 90
b = 58.382β = 90
c = 226.094γ = 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-5A1.00Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.650.5699.90.0390.0390.0430.017136.111.329697317.4
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)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.691000.2290.2290.2510.19.511.6

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 REPLACEMENTFREE R-VALUE6KFA1.650.5629697157399.850.159820.158450.18575RANDOM19.875
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]
0.50.250.5-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.579
r_dihedral_angle_3_deg14.104
r_dihedral_angle_4_deg10.916
r_dihedral_angle_1_deg6.752
r_long_range_B_refined4.962
r_long_range_B_other4.253
r_scangle_other2.09
r_scbond_it1.302
r_scbond_other1.301
r_angle_refined_deg1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.579
r_dihedral_angle_3_deg14.104
r_dihedral_angle_4_deg10.916
r_dihedral_angle_1_deg6.752
r_long_range_B_refined4.962
r_long_range_B_other4.253
r_scangle_other2.09
r_scbond_it1.302
r_scbond_other1.301
r_angle_refined_deg1.3
r_mcangle_it1.205
r_mcangle_other1.205
r_angle_other_deg0.907
r_mcbond_it0.729
r_mcbond_other0.729
r_chiral_restr0.079
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 Atoms297
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing