7SJB

Crystal structure of dehaloperoxidase B in complex with alpha-terpinene

X-RAY DIFFRACTION

---

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	277.15	MPEG 2000, ammonium sulfate, Na cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.716	α = 90
b = 67.532	β = 90
c = 67.44	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		2021-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0000	APS	22-BM

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	1.718	33.77	99.4	0.056	0.996	31.2	5		30039

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	1.72	1.762			0.803

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	1.718	33.766	30039	1466	99.401	0.161	0.1589	0.1988	28.651

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]
20.295			-5.48		-14.815

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.814
r_dihedral_angle_4_deg	23.053
r_dihedral_angle_3_deg	18.555
r_lrange_other	8.393
r_lrange_it	8.387
r_dihedral_angle_1_deg	6.909
r_scangle_it	3.519
r_scangle_other	3.514
r_mcangle_other	2.497
r_mcangle_it	2.496
r_scbond_it	2.441
r_scbond_other	2.44
r_angle_refined_deg	2.169
r_mcbond_other	1.824
r_mcbond_it	1.822
r_angle_other_deg	1.58
r_symmetry_nbd_refined	0.346
r_nbd_refined	0.289
r_symmetry_xyhbond_nbd_refined	0.258
r_symmetry_nbd_other	0.233
r_nbd_other	0.213
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.119
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2151
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	122

Software

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