2HOX

alliinase from allium sativum (garlic)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LK9PDB ENTRY 1LK9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6293PEG 4000, AMMONIUM ACETATE, TRI- SODIUM CITRATE, PH 5.6, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2444.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.665α = 90
b = 126.892β = 97.3
c = 102.664γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.3946.195.70.0490.04940.43.08327315327315-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.391.4178.10.5980.5982.12.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1LK91.446.13273153107761653596.470.169140.167240.20452RANDOM17.133
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]
-0.030.44-0.450.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.808
r_sphericity_free25.393
r_dihedral_angle_4_deg15.317
r_dihedral_angle_3_deg12.538
r_sphericity_bonded10.818
r_rigid_bond_restr6.646
r_dihedral_angle_1_deg6.113
r_scangle_it5.987
r_scbond_it4.542
r_mcangle_it2.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.808
r_sphericity_free25.393
r_dihedral_angle_4_deg15.317
r_dihedral_angle_3_deg12.538
r_sphericity_bonded10.818
r_rigid_bond_restr6.646
r_dihedral_angle_1_deg6.113
r_scangle_it5.987
r_scbond_it4.542
r_mcangle_it2.86
r_mcbond_it2.554
r_angle_refined_deg1.728
r_angle_other_deg0.991
r_mcbond_other0.529
r_symmetry_vdw_other0.284
r_symmetry_vdw_refined0.241
r_symmetry_hbond_refined0.227
r_nbd_refined0.221
r_xyhbond_nbd_refined0.211
r_nbd_other0.2
r_nbtor_refined0.189
r_chiral_restr0.109
r_nbtor_other0.093
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13748
Nucleic Acid Atoms
Solvent Atoms2669
Heterogen Atoms408

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling