6IIY

Crystal structure of deacetylase triple mutant (Orf2*T) that involving in teicoplanin biosynthetic pathway


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X9L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2M imidazole malate pH8.5, 27.5 % PEG 10000
Crystal Properties
Matthews coefficientSolvent content
2.0941.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.451α = 90
b = 66.671β = 92.59
c = 43.39γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A10.9NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.293094.743.73.963373
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)
11.291.340.98

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 REPLACEMENTTHROUGHOUT2X9L1.293058755313992.350.162760.161740.18191RANDOM17.941
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]
0.09-0.05-0.120.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.992
r_dihedral_angle_4_deg13.643
r_dihedral_angle_3_deg11.367
r_dihedral_angle_1_deg5.465
r_long_range_B_refined4.784
r_long_range_B_other4.44
r_scangle_other2.774
r_mcangle_it1.949
r_mcangle_other1.949
r_scbond_it1.778
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.992
r_dihedral_angle_4_deg13.643
r_dihedral_angle_3_deg11.367
r_dihedral_angle_1_deg5.465
r_long_range_B_refined4.784
r_long_range_B_other4.44
r_scangle_other2.774
r_mcangle_it1.949
r_mcangle_other1.949
r_scbond_it1.778
r_scbond_other1.777
r_angle_refined_deg1.382
r_mcbond_it1.193
r_mcbond_other1.187
r_angle_other_deg0.928
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.007
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 Atoms1847
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing