5KCY | pdb_00005kcy

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP628925 mM Bis-Tris, 0.2 M (NH4)2SO4, 17% PEG3350, 3.3% DDM
Crystal Properties
Matthews coefficientSolvent content
2.4349.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.95α = 90
b = 134.91β = 90
c = 68.69γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97907SSRFBL17U

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
12.3134.91970.0830.0960.047103.73945439454
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)
12.32.4293.20.2882.63.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.356.37137460195096.590.206040.203990.210.24560.25RANDOM39.09
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]
0.011.16-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.348
r_dihedral_angle_3_deg16.305
r_dihedral_angle_4_deg12.761
r_long_range_B_other8.117
r_long_range_B_refined8.115
r_dihedral_angle_1_deg6.384
r_scangle_other6.228
r_mcangle_it5.05
r_mcangle_other5.049
r_scbond_it3.927
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.348
r_dihedral_angle_3_deg16.305
r_dihedral_angle_4_deg12.761
r_long_range_B_other8.117
r_long_range_B_refined8.115
r_dihedral_angle_1_deg6.384
r_scangle_other6.228
r_mcangle_it5.05
r_mcangle_other5.049
r_scbond_it3.927
r_scbond_other3.927
r_mcbond_other3.336
r_mcbond_it3.335
r_angle_refined_deg1.843
r_angle_other_deg1.372
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms6082
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing