2JJP

Structure of cytochrome P450 EryK in complex with inhibitor ketoconazole (KC)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JJNPDB ENTRY 2JJN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52.0M AMMONIUM SULHATE, 0.1M BIS-TRIS PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.1141.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.243α = 90
b = 68.038β = 100.71
c = 57.687γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
123091.40.0516.53.925326222.73
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)
122.1585.70.1912.73.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2JJN2.156.720602110991.40.1990.1950.262RANDOM32.19
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]
-2.02-0.794.54-2.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.527
r_dihedral_angle_4_deg22.98
r_dihedral_angle_3_deg18.058
r_dihedral_angle_1_deg6.349
r_scangle_it3.475
r_scbond_it2.38
r_mcangle_it1.775
r_angle_refined_deg1.611
r_mcbond_it1.096
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.527
r_dihedral_angle_4_deg22.98
r_dihedral_angle_3_deg18.058
r_dihedral_angle_1_deg6.349
r_scangle_it3.475
r_scbond_it2.38
r_mcangle_it1.775
r_angle_refined_deg1.611
r_mcbond_it1.096
r_nbtor_refined0.313
r_nbd_refined0.238
r_xyhbond_nbd_refined0.211
r_symmetry_vdw_refined0.198
r_symmetry_hbond_refined0.168
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3079
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing