5KD6 | pdb_00005kd6

Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with dimethylallyl 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% PEG 3350, 3.3% DDM
Crystal Properties
Matthews coefficientSolvent content
2.3948.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.06α = 90
b = 134.14β = 90
c = 68.62γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.99999SSRFBL17U

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
11.84134.1499.40.0770.0880.0412.34.67711677116
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)
11.841.9499.50.3662.14.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5KCG1.8445.21973216384799.270.18210.179710.190.227850.23RANDOM26.32
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]
-0.50.280.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.461
r_dihedral_angle_4_deg16.669
r_dihedral_angle_3_deg13.71
r_long_range_B_refined6.955
r_long_range_B_other6.699
r_dihedral_angle_1_deg6.498
r_scangle_other5.048
r_scbond_it3.316
r_scbond_other3.315
r_mcangle_it3.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.461
r_dihedral_angle_4_deg16.669
r_dihedral_angle_3_deg13.71
r_long_range_B_refined6.955
r_long_range_B_other6.699
r_dihedral_angle_1_deg6.498
r_scangle_other5.048
r_scbond_it3.316
r_scbond_other3.315
r_mcangle_it3.054
r_mcangle_other3.053
r_mcbond_it2.213
r_mcbond_other2.211
r_angle_refined_deg1.878
r_angle_other_deg1.052
r_chiral_restr0.122
r_bond_refined_d0.018
r_gen_planes_refined0.011
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 Atoms6321
Nucleic Acid Atoms
Solvent Atoms654
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing