2XFH

Structure of cytochrome P450 EryK cocrystallized with inhibitor clotrimazole.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VRVPDB ENTRY 2VRV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
125% PEG 3350, 0.1M HEPES PH 7.0, 0.2M NACL
Crystal Properties
Matthews coefficientSolvent content
2.542.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.92α = 100.27
b = 53.68β = 90.93
c = 58.109γ = 94.19
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX2010-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.950940.128.82.936185120.2
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)
11.91.9784.40.372.162.8

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 2VRV1.942.7631431166593.450.183580.180940.23112RANDOM26.637
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.1
r_dihedral_angle_4_deg21.965
r_dihedral_angle_3_deg16.53
r_dihedral_angle_1_deg5.821
r_scangle_it2.721
r_scbond_it1.822
r_angle_refined_deg1.582
r_mcangle_it1.269
r_mcbond_it0.798
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.1
r_dihedral_angle_4_deg21.965
r_dihedral_angle_3_deg16.53
r_dihedral_angle_1_deg5.821
r_scangle_it2.721
r_scbond_it1.822
r_angle_refined_deg1.582
r_mcangle_it1.269
r_mcbond_it0.798
r_nbtor_refined0.31
r_symmetry_vdw_refined0.238
r_nbd_refined0.223
r_symmetry_hbond_refined0.213
r_xyhbond_nbd_refined0.171
r_chiral_restr0.103
r_bond_refined_d0.014
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 Atoms3057
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing