6EKY

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


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 = 51.18α = 90
b = 57.969β = 110.13
c = 60.975γ = 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
11.2348.0699.70.0620.0270.99913.6696881
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.231.25

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 SYNTHESISTHROUGHOUT5OXU1.2348.0692082477599.710.160550.160080.16944RANDOM15.524
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]
-0.210.63-0.920.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.971
r_dihedral_angle_4_deg17.46
r_rigid_bond_restr14.137
r_dihedral_angle_3_deg12.053
r_dihedral_angle_1_deg5.717
r_long_range_B_refined3.857
r_long_range_B_other3.856
r_sphericity_bonded3.336
r_scangle_other1.376
r_angle_refined_deg1.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.971
r_dihedral_angle_4_deg17.46
r_rigid_bond_restr14.137
r_dihedral_angle_3_deg12.053
r_dihedral_angle_1_deg5.717
r_long_range_B_refined3.857
r_long_range_B_other3.856
r_sphericity_bonded3.336
r_scangle_other1.376
r_angle_refined_deg1.359
r_angle_other_deg0.993
r_mcangle_it0.914
r_mcangle_other0.914
r_scbond_it0.843
r_scbond_other0.843
r_mcbond_it0.531
r_mcbond_other0.53
r_chiral_restr0.084
r_gen_planes_other0.008
r_bond_refined_d0.007
r_gen_planes_refined0.006
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 Atoms388
Heterogen Atoms227

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing