3O2K

Crystal Structure of Brevianamide F Prenyltransferase Complexed with Brevianamide F and Dimethylallyl S-thiolodiphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O24PDB ENTRY 3O24

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52981.3M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, VAPOR DIFFUSION, HANGING DROP. Stepwise transferred to 1.3M lithium sulfate, 0.1M MES pH 6.5, 2.5mM brevianamide F, 10mM dimethylallyl S-thiolodiphosphate for soaking, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9737.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.77α = 90
b = 82.77β = 90
c = 124.26γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2009-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
12.43099.90.0420.10929.9523.617531175183350.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.461000.2280.4078.61271258

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3O242.420317531166138741000.2090.206810.205340.23451imported from native structure, random extension to full resolution58.076
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]
-4.51-4.519.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.18
r_dihedral_angle_4_deg14.209
r_dihedral_angle_3_deg12.024
r_dihedral_angle_1_deg4.73
r_scangle_it1.498
r_mcangle_it1.051
r_scbond_it0.974
r_angle_refined_deg0.825
r_angle_other_deg0.746
r_mcbond_it0.597
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.18
r_dihedral_angle_4_deg14.209
r_dihedral_angle_3_deg12.024
r_dihedral_angle_1_deg4.73
r_scangle_it1.498
r_mcangle_it1.051
r_scbond_it0.974
r_angle_refined_deg0.825
r_angle_other_deg0.746
r_mcbond_it0.597
r_mcbond_other0.131
r_chiral_restr0.048
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3393
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing