9IFP | pdb_00009ifp

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OXU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	1.85M 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 coefficient	Solvent content
4.28	71.26

Crystal Data

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

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	KB MIRRORS	2024-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979	ALBA	XALOC

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.9	48.53	99.8	0.059	0.064	0.024	0.999	17.8	6.8		154714

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)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	99.8		1.172	1.271	0.486	0.839	1.7	6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.9	45.93	146839	7875	99.83	0.20071	0.19972	0.2081	0.21885	0.2259	RANDOM	44.174

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]
-3		0.51	3.68		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.115
r_dihedral_angle_2_deg	10.839
r_long_range_B_other	7.509
r_long_range_B_refined	7.492
r_dihedral_angle_1_deg	6.232
r_scangle_other	5.973
r_mcangle_it	4.359
r_mcangle_other	4.358
r_scbond_it	4.022
r_scbond_other	4.017
r_mcbond_it	3.193
r_mcbond_other	3.193
r_angle_refined_deg	1.413
r_angle_other_deg	0.534
r_chiral_restr	0.13
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.003
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 Atoms	Number
Protein Atoms	8398
Nucleic Acid Atoms
Solvent Atoms	705
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing