5OY2

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

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

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.115α = 90
b = 58.021β = 109.65
c = 60.853γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB mirrors2014-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9793ALBAXALOC

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
11.3648.1499.80.0840.0350.99914.96.771897
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)
11.361.3899.10.6950.2930.8623.16.5

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 SYNTHESISTHROUGHOUT5OXU1.3648.1468364351799.810.160160.159670.16961RANDOM12.6
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]
-0.440.5-0.650.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.951
r_dihedral_angle_4_deg16.24
r_dihedral_angle_3_deg12.593
r_dihedral_angle_1_deg5.454
r_long_range_B_refined3.812
r_long_range_B_other3.532
r_angle_refined_deg1.318
r_scangle_other1.178
r_mcangle_it1.029
r_mcangle_other1.029
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.951
r_dihedral_angle_4_deg16.24
r_dihedral_angle_3_deg12.593
r_dihedral_angle_1_deg5.454
r_long_range_B_refined3.812
r_long_range_B_other3.532
r_angle_refined_deg1.318
r_scangle_other1.178
r_mcangle_it1.029
r_mcangle_other1.029
r_angle_other_deg0.968
r_scbond_it0.682
r_scbond_other0.682
r_mcbond_it0.565
r_mcbond_other0.565
r_chiral_restr0.083
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 Atoms2530
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms149

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing