4XE3

OleP, the cytochrome P450 epoxidase from Streptomyces antibioticus involved in Oleandomycin biosynthesis: functional analysis and crystallographic structure in complex with clotrimazole.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y46PDB entry 2Y46

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.6 M Ammonium Sulphate, 0.1 M HEPES Sodium Salt pH 7.5, 2% (w/v) PEG 1000
Crystal Properties
Matthews coefficientSolvent content
3.463.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.937α = 90
b = 117.379β = 90
c = 174.664γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2010-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.0ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.655099.10.0940.10217.326.8834700-356.435
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.8195.40.860.9412.1

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 REPLACEMENTTHROUGHOUTPDB entry 2Y462.6548.7634700174499.130.20950.20680.2596RANDOM58.33
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]
-3.04-1.054.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.434
r_dihedral_angle_3_deg21.312
r_dihedral_angle_4_deg18.713
r_dihedral_angle_1_deg7.713
r_angle_refined_deg1.772
r_angle_other_deg0.895
r_chiral_restr0.197
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.434
r_dihedral_angle_3_deg21.312
r_dihedral_angle_4_deg18.713
r_dihedral_angle_1_deg7.713
r_angle_refined_deg1.772
r_angle_other_deg0.895
r_chiral_restr0.197
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6142
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction