9HEB | pdb_00009heb

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2911.85M ammonium sulphate, 100 mM HEPES pH 7.5; additive: 30% v/v ethylene glycol Soaking: 35 mM tetradecane 3 hours, cryoprotected with 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
4.3571.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 272.422α = 90
b = 75.256β = 111.75
c = 106.362γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB MIRRORS2021-11-19MSINGLE 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
12.5548.6998.80.1520.1690.0730.99311.95.164697
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)
12.552.6198.40.7440.8270.3570.8693.55.3

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 SYNTHESISTHROUGHOUT2.5548.6961532316598.60.190180.188370.19330.22490.2286RANDOM45.344
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]
-3.865.52-1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.348
r_long_range_B_refined7.855
r_long_range_B_other7.849
r_scangle_other6.583
r_dihedral_angle_1_deg6.498
r_dihedral_angle_2_deg5.84
r_mcangle_other4.923
r_mcangle_it4.922
r_scbond_it4.33
r_scbond_other4.242
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.348
r_long_range_B_refined7.855
r_long_range_B_other7.849
r_scangle_other6.583
r_dihedral_angle_1_deg6.498
r_dihedral_angle_2_deg5.84
r_mcangle_other4.923
r_mcangle_it4.922
r_scbond_it4.33
r_scbond_other4.242
r_mcbond_it3.203
r_mcbond_other3.201
r_angle_refined_deg1.455
r_angle_other_deg0.529
r_chiral_restr0.127
r_bond_refined_d0.007
r_gen_planes_refined0.006
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 Atoms8405
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing