6EKX

Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with 1-naphthol (I)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OXU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62911.6M sodium potassium phosphate pH 5.6, 3% MPD, soaking 100mM 1-Naphthol, 20% methanol
Crystal Properties
Matthews coefficientSolvent content
2.4249.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.086α = 90
b = 57.799β = 109.89
c = 60.691γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors2015-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9792ALBAXALOC

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
11.1348.04990.0660.0280.99913.15.9124527
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.131.140.6050.3692

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 SYNTHESISTHROUGHOUT5OXU1.1348.04118360613498.970.166420.165960.17536RANDOM12.996
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]
-0.270.45-0.680.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.44
r_rigid_bond_restr26.588
r_dihedral_angle_4_deg17.054
r_dihedral_angle_3_deg11.918
r_dihedral_angle_1_deg5.824
r_long_range_B_refined3.985
r_long_range_B_other3.985
r_sphericity_bonded3.343
r_angle_refined_deg1.351
r_scangle_other1.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.44
r_rigid_bond_restr26.588
r_dihedral_angle_4_deg17.054
r_dihedral_angle_3_deg11.918
r_dihedral_angle_1_deg5.824
r_long_range_B_refined3.985
r_long_range_B_other3.985
r_sphericity_bonded3.343
r_angle_refined_deg1.351
r_scangle_other1.175
r_angle_other_deg0.961
r_mcangle_it0.925
r_mcangle_other0.924
r_scbond_it0.723
r_scbond_other0.723
r_mcbond_other0.516
r_mcbond_it0.515
r_chiral_restr0.082
r_gen_planes_other0.009
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_bond_other_d0.004
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_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2510
Nucleic Acid Atoms
Solvent Atoms438
Heterogen Atoms206

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing