2JJO

Structure of cytochrome P450 EryK in complex with its natural substrate erD


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.525% PEG 3350, 0.2M AMMONIUM ACETATE, 0.1M TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.0539.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.84α = 90
b = 36.526β = 93.92
c = 96.004γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-01-23MSINGLE 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
123091.50.06134279532
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)
122.1580.40.2410.93.1

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 2JJN1.9995.7824282128191.50.1670.1630.227RANDOM23.2
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]
-1.21-0.540.061.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.991
r_dihedral_angle_4_deg18.496
r_dihedral_angle_3_deg15.329
r_dihedral_angle_1_deg5.71
r_scangle_it3.295
r_scbond_it2.302
r_angle_refined_deg1.577
r_mcangle_it1.439
r_angle_other_deg1.211
r_mcbond_it0.893
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.991
r_dihedral_angle_4_deg18.496
r_dihedral_angle_3_deg15.329
r_dihedral_angle_1_deg5.71
r_scangle_it3.295
r_scbond_it2.302
r_angle_refined_deg1.577
r_mcangle_it1.439
r_angle_other_deg1.211
r_mcbond_it0.893
r_nbtor_refined0.305
r_nbd_other0.257
r_nbd_refined0.213
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.148
r_nbtor_other0.126
r_chiral_restr0.102
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_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 Atoms3050
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing