9HED | pdb_00009hed

Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with alpha-damascone


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2912.15M ammonium sulphate, 100mM HEPES pH 7.5; additive: cesium chloride Soaking: 20 mM alpha-damascone 7 hours, cryoprotected with 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
4.2571.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 271.393α = 90
b = 74.362β = 111.62
c = 105.603γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB MIRRORS2021-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979ALBAXALOC

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
12.4549.1499.90.1350.1490.0630.9929.55.672203
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)
12.452.599.80.6270.6930.2890.8943.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.4549.1468656354499.840.186790.18530.19050.215310.2189RANDOM43.716
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]
-2.560.682.67-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.702
r_long_range_B_other8.217
r_long_range_B_refined8.207
r_scangle_other6.909
r_dihedral_angle_1_deg6.459
r_mcangle_it5.113
r_mcangle_other5.112
r_dihedral_angle_2_deg5.1
r_scbond_it4.597
r_scbond_other4.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.702
r_long_range_B_other8.217
r_long_range_B_refined8.207
r_scangle_other6.909
r_dihedral_angle_1_deg6.459
r_mcangle_it5.113
r_mcangle_other5.112
r_dihedral_angle_2_deg5.1
r_scbond_it4.597
r_scbond_other4.52
r_mcbond_it3.471
r_mcbond_other3.464
r_angle_refined_deg1.478
r_angle_other_deg0.531
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_gen_planes_other0.005
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 Atoms8403
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing