5B2V

Crystal Structure of P450BM3 with N-perfluorohexanoyl-L-tryptophan


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WSP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.929375mM Tris-HCl (pH7.9), 50uM N-perfluorohexanoyl L-tryptophan, 0.5% (v/v) dimethyl sulfoxide, 100mM MgCl, 10.0% (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.6653.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.881α = 90
b = 147.491β = 98.23
c = 64.247γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002014-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.000SPring-8BL26B1

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
12.35089.30.05418.93.242832
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)
12.32.3889.10.3843.2

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 REPLACEMENTTHROUGHOUT3WSP2.319.9140573217688.880.21720.21520.2546RANDOM46.705
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.485
r_dihedral_angle_3_deg12.395
r_dihedral_angle_4_deg11.768
r_dihedral_angle_1_deg5.045
r_angle_refined_deg0.935
r_angle_other_deg0.721
r_chiral_restr0.111
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.485
r_dihedral_angle_3_deg12.395
r_dihedral_angle_4_deg11.768
r_dihedral_angle_1_deg5.045
r_angle_refined_deg0.935
r_angle_other_deg0.721
r_chiral_restr0.111
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7310
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms152

Software

Software
Software NamePurpose
DENZOdata collection
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction