3ZKP

Structure of a mutant of P450 EryK in complex with erythromycin B.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JJOPDB ENTRY 2JJO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.525% PEG3350, 0.1 M TRIS HCL, PH 8.5, 0.2 M CH3COONH4
Crystal Properties
Matthews coefficientSolvent content
1.9134.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.753α = 90
b = 36.597β = 92.93
c = 96.273γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
123098.30.09133.9277741
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)
122.0377.40.442.13.1

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2JJO229.1225901136798.150.165970.163320.21529RANDOM17.191
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.496
r_dihedral_angle_4_deg16.432
r_dihedral_angle_3_deg14.592
r_dihedral_angle_1_deg5.149
r_scangle_it1.981
r_angle_refined_deg1.41
r_scbond_it1.397
r_mcangle_it0.988
r_mcbond_it0.604
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.496
r_dihedral_angle_4_deg16.432
r_dihedral_angle_3_deg14.592
r_dihedral_angle_1_deg5.149
r_scangle_it1.981
r_angle_refined_deg1.41
r_scbond_it1.397
r_mcangle_it0.988
r_mcbond_it0.604
r_nbtor_refined0.302
r_nbd_refined0.203
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.172
r_symmetry_hbond_refined0.156
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms3030
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms93

Software

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