8RNK

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629125% PEG 4000, 100mM sodium acetate pH 4.6, 200mM ammonium sulfate. Soaking: 10 mM myristic acid, 4 hours, cryoprotected with 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.448.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.5α = 90
b = 75.5β = 90
c = 186.049γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB MIRRORS2021-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9792ALBAXALOC

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
11.647.9799.60.0450.0480.0180.99918.86.771442
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)
11.61.631000.6010.6610.2720.8922.15.7

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 REPLACEMENTTHROUGHOUT1.647.9767942345799.360.170980.169850.19297RANDOM24.249
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]
0.810.81-1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.508
r_dihedral_angle_2_deg6.639
r_dihedral_angle_1_deg6.566
r_long_range_B_refined4.744
r_long_range_B_other4.662
r_scangle_other3.82
r_scbond_it2.538
r_scbond_other2.527
r_mcangle_it2.429
r_mcangle_other2.429
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.508
r_dihedral_angle_2_deg6.639
r_dihedral_angle_1_deg6.566
r_long_range_B_refined4.744
r_long_range_B_other4.662
r_scangle_other3.82
r_scbond_it2.538
r_scbond_other2.527
r_mcangle_it2.429
r_mcangle_other2.429
r_mcbond_it1.641
r_mcbond_other1.637
r_angle_refined_deg1.395
r_angle_other_deg0.522
r_chiral_restr0.07
r_gen_planes_other0.011
r_gen_planes_refined0.008
r_bond_refined_d0.007
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 Atoms3894
Nucleic Acid Atoms
Solvent Atoms476
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing