9HE9 | pdb_00009he9

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2911.9M ammonium sulphate, 100 mM HEPES pH 7.5 Soaking: 10 mM lauric acid 4 hours, cryoprotected with 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
4.2571.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 271.878α = 90
b = 75.001β = 111.74
c = 105.446γ = 90
Symmetry
Space GroupC 1 2 1

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 XALOC0.979ALBAXALOC

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
12.1548.3799.90.1290.1410.0550.9947.56.4107314
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)
12.152.1999.90.6320.6860.2630.9352.16.8

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 SYNTHESISTHROUGHOUT2.1548.37101822548999.840.200020.198580.20510.226890.2344RANDOM46.423
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]
-1.781.622.4-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.468
r_long_range_B_refined6.639
r_long_range_B_other6.614
r_dihedral_angle_1_deg6.269
r_scangle_other5.16
r_dihedral_angle_2_deg4.9
r_mcangle_it4.046
r_mcangle_other4.046
r_scbond_it3.38
r_scbond_other3.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.468
r_long_range_B_refined6.639
r_long_range_B_other6.614
r_dihedral_angle_1_deg6.269
r_scangle_other5.16
r_dihedral_angle_2_deg4.9
r_mcangle_it4.046
r_mcangle_other4.046
r_scbond_it3.38
r_scbond_other3.307
r_mcbond_it2.726
r_mcbond_other2.726
r_angle_refined_deg1.267
r_angle_other_deg0.469
r_chiral_restr0.122
r_bond_refined_d0.005
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 Atoms8337
Nucleic Acid Atoms
Solvent Atoms738
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing