3IE5

Crystal structure of Hyp-1 protein from Hypericum perforatum (St John's wort) involved in hypericin biosynthesis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XDFPDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0
experimental modelPDB 2QIMPDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0
experimental modelPDB 2FLHPDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0
experimental modelPDB 1TW0PDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0
experimental modelPDB 2BK0PDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52920.4M NaCl, 0.1M Tris/HCl, 30% (w/v) PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.3347.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.538α = 90
b = 76.713β = 90
c = 119.799γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2008-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.688301000.07821.473981339813-320.58
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)
1.6881.7599.90.662.25.43912

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 REPLACEMENTR-freePDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK01.68827.6631.343974239742159099.890.1720.1720.170.206random27.532
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]
4.87544.6346-9.51
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.846
f_angle_d1.525
f_chiral_restr0.11
f_bond_d0.015
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2737
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms140

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling