5JTD

Crystal structure of the Ru(bpy)2PhenA functionalized P450 BM3 L407C heme domain mutant in complex with DMSO.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JPZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293150 mM MgCl2, 125 mM Na-MOPS, 20% PEG 3350, cryo: 30% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.5451.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.69α = 90
b = 145.39β = 97.08
c = 62.9γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.447.3679.50.0440.9989.613.2183724-324.898
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)
11.41.548.10.8290.96

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 REPLACEMENTTHROUGHOUT1JPZ1.547.36153091805896.750.17450.17330.1977RANDOM22.68
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]
-0.9-0.26-0.651.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.78
r_dihedral_angle_4_deg14.865
r_dihedral_angle_3_deg11.79
r_dihedral_angle_1_deg6.074
r_mcangle_it2.117
r_angle_refined_deg1.561
r_mcbond_it1.361
r_mcbond_other1.36
r_angle_other_deg0.961
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.78
r_dihedral_angle_4_deg14.865
r_dihedral_angle_3_deg11.79
r_dihedral_angle_1_deg6.074
r_mcangle_it2.117
r_angle_refined_deg1.561
r_mcbond_it1.361
r_mcbond_other1.36
r_angle_other_deg0.961
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7368
Nucleic Acid Atoms
Solvent Atoms699
Heterogen Atoms188

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction