5OXU

Direct-evolutioned unspecific peroxygenase from Agrocybe aegerita


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62911.6M sodium potassium phosphate pH 5.6, 3% MPD
Crystal Properties
Matthews coefficientSolvent content
2.4249.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.072α = 90
b = 57.939β = 109.36
c = 61.099γ = 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)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
11.4748.1992.90.0960.070.9927.72.453236
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)
11.471.593.40.650.520.6242.52.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5OXT1.4748.1950634259392.870.164460.163730.17836RANDOM11.654
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]
-0.520.55-0.830.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.631
r_dihedral_angle_4_deg13.866
r_dihedral_angle_3_deg11.934
r_dihedral_angle_1_deg5.691
r_long_range_B_refined3.725
r_long_range_B_other3.725
r_angle_refined_deg1.298
r_scangle_other1.021
r_angle_other_deg0.948
r_mcangle_it0.841
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.631
r_dihedral_angle_4_deg13.866
r_dihedral_angle_3_deg11.934
r_dihedral_angle_1_deg5.691
r_long_range_B_refined3.725
r_long_range_B_other3.725
r_angle_refined_deg1.298
r_scangle_other1.021
r_angle_other_deg0.948
r_mcangle_it0.841
r_mcangle_other0.84
r_scbond_it0.602
r_scbond_other0.602
r_mcbond_it0.465
r_mcbond_other0.464
r_chiral_restr0.071
r_gen_planes_other0.007
r_bond_refined_d0.006
r_gen_planes_refined0.006
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 Atoms2514
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms158

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing