5KCQ

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


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
2.4349.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.33α = 90
b = 135.67β = 90
c = 68.61γ = 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
12135.6791.30.1060.1190.0539.94.35564055640
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)
122.1185.80.3082.24.5

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 REPLACEMENTTHROUGHOUT5KCG248.2452816279390.420.187760.185860.22356RANDOM23.118
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]
-0.440.54-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.094
r_dihedral_angle_3_deg14.605
r_dihedral_angle_4_deg14.44
r_dihedral_angle_1_deg6.076
r_long_range_B_refined6.051
r_long_range_B_other6.034
r_scangle_other4.821
r_scbond_it3.206
r_scbond_other3.206
r_mcangle_it2.831
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.094
r_dihedral_angle_3_deg14.605
r_dihedral_angle_4_deg14.44
r_dihedral_angle_1_deg6.076
r_long_range_B_refined6.051
r_long_range_B_other6.034
r_scangle_other4.821
r_scbond_it3.206
r_scbond_other3.206
r_mcangle_it2.831
r_mcangle_other2.831
r_mcbond_it2.023
r_mcbond_other2.022
r_angle_refined_deg1.911
r_angle_other_deg1.323
r_chiral_restr0.117
r_bond_refined_d0.024
r_gen_planes_refined0.011
r_bond_other_d0.007
r_gen_planes_other0.006
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 Atoms6301
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing