9HEA | pdb_00009hea

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2911.95M ammonium sulphate, 100 mM HEPES pH 7.5; additive: spermine tetrahydrochloride Soaking: 25 mM myristic acid 4 hours, cryoprotected with 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
4.2671.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 271.504α = 90
b = 74.713β = 111.7
c = 106.253γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB MIRRORS2021-07-22MSINGLE 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
12.5549.4199.80.1220.1320.0520.99612.16.664666
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)
12.552.611000.7060.7640.2890.933.77

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 SYNTHESISTHROUGHOUT2.5549.4161359329099.690.186760.185280.19120.213570.2188RANDOM50.397
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]
-3.50.344.07-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.856
r_long_range_B_other8.338
r_long_range_B_refined8.334
r_scangle_other6.62
r_dihedral_angle_1_deg6.449
r_dihedral_angle_2_deg5.168
r_mcangle_it4.945
r_mcangle_other4.945
r_scbond_it4.341
r_scbond_other4.284
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.856
r_long_range_B_other8.338
r_long_range_B_refined8.334
r_scangle_other6.62
r_dihedral_angle_1_deg6.449
r_dihedral_angle_2_deg5.168
r_mcangle_it4.945
r_mcangle_other4.945
r_scbond_it4.341
r_scbond_other4.284
r_mcbond_it3.296
r_mcbond_other3.292
r_angle_refined_deg1.343
r_angle_other_deg0.483
r_chiral_restr0.127
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d0.002
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 Atoms8440
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing