5KDA

Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with dimethylallyl S-thiolodiphosphate and genistein


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62890.1 M Bis-Tris pH 6.0, 0.2 M (NH4)2SO4, 17% PEG 3350, 3.3% DDM
Crystal Properties
Matthews coefficientSolvent content
2.550.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.65α = 90
b = 136.08β = 90
c = 68.84γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.99999SSRFBL17U

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
1278.888.974.252312
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.11

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 REPLACEMENTTHROUGHOUT5KCG278.852312273188.620.190950.188480.23772RANDOM26.121
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]
-0.680.94-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.593
r_dihedral_angle_4_deg16.469
r_dihedral_angle_3_deg15.802
r_dihedral_angle_1_deg6.715
r_long_range_B_refined6.203
r_long_range_B_other6.137
r_scangle_other4.657
r_scbond_it3.059
r_scbond_other3.059
r_mcangle_it3.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.593
r_dihedral_angle_4_deg16.469
r_dihedral_angle_3_deg15.802
r_dihedral_angle_1_deg6.715
r_long_range_B_refined6.203
r_long_range_B_other6.137
r_scangle_other4.657
r_scbond_it3.059
r_scbond_other3.059
r_mcangle_it3.056
r_mcangle_other3.056
r_mcbond_it2.148
r_mcbond_other2.148
r_angle_refined_deg1.884
r_angle_other_deg1.062
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.01
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 Atoms6311
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
Cootmodel building
SCALAdata scaling