9IFP | pdb_00009ifp

Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with 2,6-dimethoxyphenol


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, 0.1M HEPES pH 7.5, additive: 30% v/v ethylene glycol Soaking: 25 mM 2,6-dimethoxyphenol 2h30, cryoprotected with 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
4.2871.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 271.298α = 90
b = 74.502β = 111.8
c = 106.15γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKB MIRRORS2024-02-01MSINGLE 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
11.948.5399.80.0590.0640.0240.99917.86.8154714
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)
11.91.9399.81.1721.2710.4860.8391.76.7

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 SYNTHESISTHROUGHOUT1.945.93146839787599.830.200710.199720.20810.218850.2259RANDOM44.174
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]
-30.513.68-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.115
r_dihedral_angle_2_deg10.839
r_long_range_B_other7.509
r_long_range_B_refined7.492
r_dihedral_angle_1_deg6.232
r_scangle_other5.973
r_mcangle_it4.359
r_mcangle_other4.358
r_scbond_it4.022
r_scbond_other4.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.115
r_dihedral_angle_2_deg10.839
r_long_range_B_other7.509
r_long_range_B_refined7.492
r_dihedral_angle_1_deg6.232
r_scangle_other5.973
r_mcangle_it4.359
r_mcangle_other4.358
r_scbond_it4.022
r_scbond_other4.017
r_mcbond_it3.193
r_mcbond_other3.193
r_angle_refined_deg1.413
r_angle_other_deg0.534
r_chiral_restr0.13
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d0.003
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 Atoms8398
Nucleic Acid Atoms
Solvent Atoms705
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing