9RG3 | pdb_00009rg3

Unspecific peroxygenase from Psathyrella aberdarensis, Grogu variant, in complex with anisole

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9HE6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	10% (v/v) PEG 8000, 100mM MES pH 6.5, 200mM Zn acetate Additive: 100mM magnesium chloride Soaking 30mM anisole (time: 2h45)

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.785	α = 90
b = 75.785	β = 90
c = 273.418	γ = 120

Symmetry
Space Group	P 65

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	2023-04-21	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	2.5	47.39	99.9	0.077	0.084	0.032	0.998	14.3	6.8		30804

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	2.5	2.6	99.9		0.612	0.663	0.253	0.86	2.2	6.8

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.5	47.39	29148	1570	99.86	0.21674	0.21432	0.2168	0.26232	0.2626	RANDOM	54.755

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]
-0.56	-0.28		-0.56		1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.909
r_long_range_B_refined	9.802
r_long_range_B_other	9.779
r_dihedral_angle_1_deg	7.124
r_scangle_other	7.051
r_mcangle_it	6.81
r_mcangle_other	6.809
r_dihedral_angle_2_deg	6.308
r_scbond_it	4.65
r_scbond_other	4.65
r_mcbond_other	4.518
r_mcbond_it	4.517
r_angle_refined_deg	1.364
r_angle_other_deg	0.482
r_chiral_restr	0.064
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_gen_planes_other	0.005
r_bond_other_d	0.001
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	5176
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	365

Software

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