8RNO

Unspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in complex with isophorone


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29112% PEG 4000, 200mM ammonium sulfate. Soaking: 30 mM isophorone, 16 hours, cryoprotected with 15% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4549.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.233α = 90
b = 76.233β = 90
c = 185.484γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB MIRRORS2021-05-22MSINGLE 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)Rrim I (All)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
12.0548.0795.20.0510.0550.0190.99916.46.733452
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1197.60.5580.6020.2140.9222.36.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.0548.0731696167894.670.203960.201560.24785RANDOM53.954
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]
2.482.48-4.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.443
r_dihedral_angle_2_deg8.994
r_long_range_B_other7.914
r_long_range_B_refined7.904
r_dihedral_angle_1_deg6.357
r_scangle_other6.25
r_mcangle_it5.568
r_mcangle_other5.567
r_scbond_it4.374
r_scbond_other4.346
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.443
r_dihedral_angle_2_deg8.994
r_long_range_B_other7.914
r_long_range_B_refined7.904
r_dihedral_angle_1_deg6.357
r_scangle_other6.25
r_mcangle_it5.568
r_mcangle_other5.567
r_scbond_it4.374
r_scbond_other4.346
r_mcbond_it4.208
r_mcbond_other4.208
r_angle_refined_deg1.294
r_angle_other_deg0.443
r_chiral_restr0.064
r_gen_planes_other0.008
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_bond_other_d0.001
r_dihedral_angle_4_deg
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 Atoms3853
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing