7SJG

Structure of Dehaloperoxidase B in Complex with Thymoquinone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IXF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	MPEG 2000, ammonium sulfate, Na cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.358	α = 90
b = 67.565	β = 90
c = 67.825	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300-HS		2021-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.000	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	44.2	99.9	0.999	17.1	4.7		53478

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.436			0.541

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3IXF	1.4	44.2	53478	2686	99.923	0.145	0.1424	0.1949	21.02

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]
2.294			-3.379		1.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.051
r_dihedral_angle_4_deg	22.573
r_dihedral_angle_3_deg	17.134
r_scangle_other	10.011
r_scangle_it	9.995
r_lrange_it	8.968
r_lrange_other	8.922
r_scbond_other	8.901
r_scbond_it	8.884
r_dihedral_angle_1_deg	6.005
r_rigid_bond_restr	5.314
r_mcangle_other	4.505
r_mcangle_it	4.501
r_mcbond_it	3.714
r_mcbond_other	3.713
r_angle_refined_deg	2.258
r_angle_other_deg	1.704
r_dihedral_angle_other_3_deg	1.17
r_symmetry_nbd_refined	0.306
r_nbd_other	0.296
r_nbd_refined	0.295
r_symmetry_xyhbond_nbd_other	0.27
r_symmetry_nbd_other	0.23
r_xyhbond_nbd_refined	0.211
r_symmetry_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.194
r_chiral_restr	0.119
r_symmetry_nbtor_other	0.091
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_gen_planes_other	0.006
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2133
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	204

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing