5O4L

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherInhouse

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
2.6553.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.53α = 90
b = 77.53β = 90
c = 264.95γ = 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
11.6467.141000.1690.0410.9912.51958784
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)
11.641.71001.940.4510.4861.720

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 REPLACEMENTTHROUGHOUTInhouse1.6467.1456784200099.850.163580.162630.19048RANDOM23.93
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]
-0.14-0.07-0.140.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.305
r_dihedral_angle_4_deg16.437
r_dihedral_angle_3_deg12.854
r_long_range_B_refined8.066
r_long_range_B_other7.946
r_scangle_other6.735
r_dihedral_angle_1_deg5.327
r_scbond_it4.911
r_scbond_other4.91
r_mcangle_other2.485
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.305
r_dihedral_angle_4_deg16.437
r_dihedral_angle_3_deg12.854
r_long_range_B_refined8.066
r_long_range_B_other7.946
r_scangle_other6.735
r_dihedral_angle_1_deg5.327
r_scbond_it4.911
r_scbond_other4.91
r_mcangle_other2.485
r_mcangle_it2.484
r_mcbond_it1.893
r_mcbond_other1.891
r_angle_refined_deg1.682
r_angle_other_deg1.51
r_chiral_restr0.109
r_bond_refined_d0.016
r_gen_planes_refined0.01
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 Atoms402
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing