8Q22

Crystal structure of Vanadium-dependent haloperoxidase R425S mutant in complex with 1,3,5-trimethoxybenzene (A. marina)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LPC	Crystal structure of Vanadium-dependent Haloperoxidase from A. marina

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.1 M TRIS, 1.25 M ammoniumdihydrogenphosphate, 0.5 mM potassium vanadate, 10 mM 1,3,5-trimethoxybenzene

Crystal Properties
Matthews coefficient	Solvent content
4.08	69.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 305.8	α = 90
b = 305.8	β = 90
c = 305.8	γ = 90

Symmetry
Space Group	F 41 3 2

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		2019-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.3	30	94.3	0.108	9.6	4.5		17934

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.4			0.629	2

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	3.3	30	17015	895	94.22	0.218	0.2163	0.2485	RANDOM	83.809

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.651
r_dihedral_angle_3_deg	15.083
r_dihedral_angle_4_deg	12.925
r_dihedral_angle_1_deg	5.056
r_angle_refined_deg	1.191
r_angle_other_deg	1.046
r_rigid_bond_restr	0.119
r_chiral_restr	0.034
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.651
r_dihedral_angle_3_deg	15.083
r_dihedral_angle_4_deg	12.925
r_dihedral_angle_1_deg	5.056
r_angle_refined_deg	1.191
r_angle_other_deg	1.046
r_rigid_bond_restr	0.119
r_chiral_restr	0.034
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4931
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	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 R01GM133198.