9RG2 | pdb_00009rg2

Unspecific peroxygenase from Psathyrella aberdarensis, Grogu variant, in complex with alpha-damascone

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	11% (v/v) PEG 8000, 100mM MES pH 6.5, 150mM Zn chloride Cocrystallization 45mM alpha-damascone (incubation time: 35 minutes)

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.33	α = 90
b = 76.33	β = 90
c = 272.231	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	2023-09-14	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	1.8	47.46	99.8	0.067	0.072	0.027	0.999	16.7	6.8		83156

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	1.8	1.83	98.4		0.614	0.665	0.254	0.853	2.7	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	47.46	78961	4074	99.79	0.15615	0.15468	0.1643	0.18532	0.1943	RANDOM	22.738

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]
0.3	0.15		0.3		-0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.514
r_dihedral_angle_2_deg	8.134
r_dihedral_angle_1_deg	6.341
r_long_range_B_other	5.699
r_long_range_B_refined	5.697
r_scangle_other	4.378
r_scbond_it	2.902
r_scbond_other	2.887
r_mcangle_it	2.544
r_mcangle_other	2.544
r_mcbond_it	1.808
r_mcbond_other	1.807
r_angle_refined_deg	1.534
r_angle_other_deg	0.639
r_chiral_restr	0.082
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.008
r_bond_other_d	0.007
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	5364
Nucleic Acid Atoms
Solvent Atoms	853
Heterogen Atoms	208

Software

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