5OY1

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62911.8M sodium potassium phosphate pH 5.6, 3% MPD, 20% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.4249.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.084α = 90
b = 58.074β = 109.94
c = 60.811γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MKB mirrors2015-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9787ALBAXALOC

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
11.4348.021000.0840.0350.99915.26.761836
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)
11.431.451000.6720.2790.8152.86.7

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 SYNTHESISTHROUGHOUT5OXU1.4348.0258821299699.950.15310.152220.17013RANDOM13.241
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]
-0.540.35-0.350.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.719
r_dihedral_angle_4_deg16.402
r_dihedral_angle_3_deg11.919
r_dihedral_angle_1_deg5.621
r_long_range_B_refined4.274
r_long_range_B_other4.274
r_angle_refined_deg1.292
r_scangle_other1.023
r_angle_other_deg0.963
r_mcangle_it0.844
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.719
r_dihedral_angle_4_deg16.402
r_dihedral_angle_3_deg11.919
r_dihedral_angle_1_deg5.621
r_long_range_B_refined4.274
r_long_range_B_other4.274
r_angle_refined_deg1.292
r_scangle_other1.023
r_angle_other_deg0.963
r_mcangle_it0.844
r_mcangle_other0.844
r_scbond_it0.615
r_scbond_other0.615
r_mcbond_it0.468
r_mcbond_other0.467
r_chiral_restr0.071
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2521
Nucleic Acid Atoms
Solvent Atoms430
Heterogen Atoms176

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing