5O4K

Crystal structure of P450 CYP121 in complex with compound 6b.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N40 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2771.5 to 2.1 M ammonium sulfate and 0.1 M sodium MES or Cacodylate from pH 5.5 to 6.15
Crystal Properties
Matthews coefficientSolvent content
2.6553.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.625α = 90
b = 77.625β = 90
c = 264.291γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.567.231000.1110.0260.9918.11976451
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.561001.060.2430.909320

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 REPLACEMENTTHROUGHOUT1N401.567.2374708200099.940.151520.150930.17354RANDOM19.999
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]
-0.05-0.03-0.050.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.229
r_dihedral_angle_4_deg15.769
r_dihedral_angle_3_deg13.071
r_long_range_B_refined5.956
r_long_range_B_other5.742
r_dihedral_angle_1_deg5.39
r_scangle_other4.278
r_scbond_it2.987
r_scbond_other2.987
r_angle_refined_deg1.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.229
r_dihedral_angle_4_deg15.769
r_dihedral_angle_3_deg13.071
r_long_range_B_refined5.956
r_long_range_B_other5.742
r_dihedral_angle_1_deg5.39
r_scangle_other4.278
r_scbond_it2.987
r_scbond_other2.987
r_angle_refined_deg1.958
r_mcangle_it1.811
r_mcangle_other1.81
r_mcbond_it1.249
r_mcbond_other1.249
r_angle_other_deg1.074
r_chiral_restr0.127
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_gen_planes_other0.007
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3031
Nucleic Acid Atoms
Solvent Atoms510
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing