8OMC

Y345F/F347Y/Y389F Variant of Dye Type Peroxidase Aa (DtpAa) from Streptomyces lividans

X-RAY DIFFRACTION

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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	VAPOR DIFFUSION, HANGING DROP		291	1:1 RATIO OF A 15 MG/ML PROTEIN SOLUTION WITH A PRECIPITANT SOLUTION CONTAINING 20% PEG 6000, 100 MM HEPES PH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.852	α = 90
b = 67.93	β = 105.46
c = 74.483	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 EIGER X 16M		2022-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.98	Diamond	I04

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	1.5	58.26	100	0.078	0.092	0.049	0.999	10.9	6.9		110533

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	1.5	1.53			1.336	1.582	0.84	0.558		6.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.5	58.26	105042	5468	100	0.1622	0.16078	0.18922	RANDOM	18.962

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]
0.28		0.12	-1.2		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.43
r_dihedral_angle_3_deg	13.115
r_dihedral_angle_1_deg	6.991
r_long_range_B_refined	5.408
r_long_range_B_other	5.364
r_scangle_other	4.396
r_scbond_other	3.194
r_scbond_it	3.193
r_mcangle_other	2.915
r_mcangle_it	2.914
r_mcbond_it	2.239
r_mcbond_other	2.237
r_angle_refined_deg	2.005
r_angle_other_deg	0.685
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
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	5579
Nucleic Acid Atoms
Solvent Atoms	648
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
Aimless	data scaling
REFMAC	phasing