6EKW

Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita, in complex with naphthalene


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62911.4M sodium potassium phosphate pH 5.6, 3% MPD, soaking 20mM naphthalene, 20% methanol
Crystal Properties
Matthews coefficientSolvent content
2.4249.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.187α = 90
b = 57.743β = 109.46
c = 61.104γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors2015-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9795ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.4348.2698.50.0890.0430.99710.84.961029
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.431.45910.6510.3490.75224.1

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 SYNTHESISTHROUGHOUT5OXU1.4348.2657996301398.240.156590.155380.18024RANDOM14.306
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]
-0.370.39-0.960.84
RMS Deviations
KeyRefinement Restraint Deviation
r_rigid_bond_restr39.666
r_dihedral_angle_2_deg33.423
r_dihedral_angle_4_deg17.276
r_dihedral_angle_3_deg11.861
r_dihedral_angle_1_deg5.684
r_sphericity_bonded4.497
r_long_range_B_refined4.399
r_long_range_B_other4.123
r_scangle_other1.408
r_angle_refined_deg1.405
RMS Deviations
KeyRefinement Restraint Deviation
r_rigid_bond_restr39.666
r_dihedral_angle_2_deg33.423
r_dihedral_angle_4_deg17.276
r_dihedral_angle_3_deg11.861
r_dihedral_angle_1_deg5.684
r_sphericity_bonded4.497
r_long_range_B_refined4.399
r_long_range_B_other4.123
r_scangle_other1.408
r_angle_refined_deg1.405
r_angle_other_deg1.243
r_mcangle_it0.976
r_mcangle_other0.976
r_scbond_it0.854
r_scbond_other0.853
r_mcbond_it0.592
r_mcbond_other0.575
r_chiral_restr0.084
r_gen_planes_other0.011
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms2514
Nucleic Acid Atoms
Solvent Atoms447
Heterogen Atoms202

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing