5KD0

Crystal structure of the aromatic prenyltransferase AtaPT(E91A) mutant from Aspergillus terreus A8-4 in complex with geranyl S-thiolodiphosphate and (+)-butyrolactone II


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5KCG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP628925 mM Bis-Tris pH 6.0, 0.2 M (NH4)2SO4, 17% PEG3350, 3.3% DDM
Crystal Properties
Matthews coefficientSolvent content
2.5151.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.69α = 90
b = 139.24β = 90
c = 68.8γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-12-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97892SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.82139.2498.80.0930.0990.03415.88.12277622776
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.822.9798.40.38127.7

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 REPLACEMENTTHROUGHOUT5KCG2.82139.2421593114498.50.208090.204940.26791RANDOM41.605
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]
0.09-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.545
r_dihedral_angle_3_deg18.181
r_dihedral_angle_4_deg16.406
r_long_range_B_refined6.41
r_long_range_B_other6.41
r_dihedral_angle_1_deg6.081
r_scangle_other4.218
r_mcangle_it3.868
r_mcangle_other3.868
r_scbond_it2.518
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.545
r_dihedral_angle_3_deg18.181
r_dihedral_angle_4_deg16.406
r_long_range_B_refined6.41
r_long_range_B_other6.41
r_dihedral_angle_1_deg6.081
r_scangle_other4.218
r_mcangle_it3.868
r_mcangle_other3.868
r_scbond_it2.518
r_scbond_other2.518
r_mcbond_it2.392
r_mcbond_other2.392
r_angle_other_deg2.201
r_angle_refined_deg1.903
r_chiral_restr0.09
r_bond_refined_d0.019
r_bond_other_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.007
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 Atoms6293
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing