5JQ2

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


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.5151.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.88α = 90
b = 112.54β = 90
c = 156.36γ = 90
Symmetry
Space GroupP 21 21 21

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
11.947.5499.20.1290.99710.47583423-331.496
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)
11.9299.51.1041.4

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 REPLACEMENTTHROUGHOUT3NPL247.5468037358199.130.17640.17420.2181RANDOM29.25
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]
-0.991.07-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.891
r_dihedral_angle_4_deg15.433
r_dihedral_angle_3_deg14.034
r_dihedral_angle_1_deg6.633
r_mcangle_it3.352
r_mcbond_it2.231
r_mcbond_other2.229
r_angle_refined_deg1.817
r_angle_other_deg1.039
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.891
r_dihedral_angle_4_deg15.433
r_dihedral_angle_3_deg14.034
r_dihedral_angle_1_deg6.633
r_mcangle_it3.352
r_mcbond_it2.231
r_mcbond_other2.229
r_angle_refined_deg1.817
r_angle_other_deg1.039
r_chiral_restr0.113
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7367
Nucleic Acid Atoms
Solvent Atoms491
Heterogen Atoms216

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction