7SJF

Structure of Dehaloperoxidase B in Complex with Thymol

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		277	MPEG 2000, ammonium sulfate, Na cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.316	α = 90
b = 66.898	β = 90
c = 67.615	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	1.81	37.344	83.07	0.998	22.1	4.2		20141

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	1.811	1.858			0.793

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	1.96	37.344	16575	838	81.9	0.211	0.2066	0.2912	31.51

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]
19.955			-13.75		-6.205

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.238
r_dihedral_angle_4_deg	21.65
r_dihedral_angle_3_deg	20.606
r_dihedral_angle_1_deg	7.428
r_lrange_other	6.225
r_lrange_it	6.224
r_scangle_it	2.504
r_scangle_other	2.478
r_mcangle_other	2.384
r_mcangle_it	2.383
r_angle_refined_deg	1.865
r_scbond_it	1.735
r_scbond_other	1.715
r_mcbond_it	1.65
r_mcbond_other	1.649
r_angle_other_deg	1.441
r_symmetry_xyhbond_nbd_other	0.285
r_nbd_refined	0.266
r_symmetry_nbd_other	0.226
r_xyhbond_nbd_refined	0.22
r_symmetry_xyhbond_nbd_refined	0.203
r_nbd_other	0.19
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.175
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2152
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing