8PXP | pdb_00008pxp

Compound II structure of Y389F variant of A type dye-decolourising peroxidase DtpAa

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6TB8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7	293	1:1 v/v solutions of 6.2 mg/ Y389F DtpAa in 20 mM sodium phosphate, 150 mM NaCl pH 7 with a precipitant solution consisting of 100 mM HEPES pH 7, 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.939	α = 90
b = 67.543	β = 104.77
c = 70.797	γ = 90

Symmetry
Space Group	P 1 21 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-F		2022-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.8	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.01	48.08	99	0.316	0.958	8.9	5.2		45274

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.01	2.04			1.174	0.368	2.9

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	2.01	43.88	45241	2186	99.06	0.21003	0.21	0.2083	0.25	0.256	RANDOM	23.522

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]
-0.06		-0.48	-0.53		0.74

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.054
f_angle_d	0.765
f_chiral_restr	0.044
f_plane_restr	0.009
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5562
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
xia2.multiplex	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.