3O24 | pdb_00003o24

Crystal structure of the brevianamide F prenyltransferase FtmPT1 from Aspergillus fumigatus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I4ZPDB ENTRY 3I4Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52981.3M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9436.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.85α = 90
b = 82.85β = 90
c = 121.76γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0000SLSX06DA

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
12.53096.40.0720.10213.799.315277147213347
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)
2.52.571000.2540.325.489.81091

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3I4Z2.5203146901395773396.450.2190.1890.186420.190.23650.23RANDOM51.092
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]
-3.61-3.617.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.881
r_dihedral_angle_4_deg18.092
r_dihedral_angle_3_deg16.589
r_dihedral_angle_1_deg5.793
r_scangle_it3.335
r_mcangle_it2.724
r_scbond_it2.347
r_mcbond_it1.77
r_angle_refined_deg1.155
r_angle_other_deg0.844
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.881
r_dihedral_angle_4_deg18.092
r_dihedral_angle_3_deg16.589
r_dihedral_angle_1_deg5.793
r_scangle_it3.335
r_mcangle_it2.724
r_scbond_it2.347
r_mcbond_it1.77
r_angle_refined_deg1.155
r_angle_other_deg0.844
r_mcbond_other0.588
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms3419
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms21

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling