8RNJ

Unspecific peroxygenase from Marasmius wettsteinii (MweUPO-1)


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 400, 100 mM sodium acetate pH 4.6, 100 mM magnesium chloride.
Crystal Properties
Matthews coefficientSolvent content
2.3246.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.574α = 90
b = 73.574β = 90
c = 186.671γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB MIRRORS2021-03-05MSINGLE 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
11.647.5699.70.0550.0590.0220.99916.57.367994
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)
11.61.6398.20.6910.7480.280.8672.87

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 REPLACEMENTTHROUGHOUT1.647.5664464345899.50.168870.167330.19771RANDOM23.091
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]
0.820.82-1.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.612
r_dihedral_angle_2_deg10.26
r_dihedral_angle_1_deg6.18
r_long_range_B_refined4.668
r_long_range_B_other4.668
r_scangle_other3.665
r_mcangle_other2.506
r_mcangle_it2.505
r_scbond_it2.391
r_scbond_other2.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.612
r_dihedral_angle_2_deg10.26
r_dihedral_angle_1_deg6.18
r_long_range_B_refined4.668
r_long_range_B_other4.668
r_scangle_other3.665
r_mcangle_other2.506
r_mcangle_it2.505
r_scbond_it2.391
r_scbond_other2.39
r_mcbond_it1.663
r_mcbond_other1.662
r_angle_refined_deg1.457
r_angle_other_deg0.824
r_chiral_restr0.07
r_gen_planes_other0.012
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.004
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 Atoms3642
Nucleic Acid Atoms
Solvent Atoms444
Heterogen Atoms206

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing